Starting phenix.real_space_refine on Thu Dec 7 20:45:16 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uae_26422/12_2023/7uae_26422.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uae_26422/12_2023/7uae_26422.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uae_26422/12_2023/7uae_26422.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uae_26422/12_2023/7uae_26422.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uae_26422/12_2023/7uae_26422.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uae_26422/12_2023/7uae_26422.pdb" } resolution = 2.6 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= 0.044 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 2834 2.51 5 N 748 2.21 5 O 907 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 69": "NH1" <-> "NH2" Residue "A ARG 74": "NH1" <-> "NH2" Residue "A GLU 166": "OE1" <-> "OE2" Residue "A GLU 251": "OE1" <-> "OE2" Residue "A ARG 252": "NH1" <-> "NH2" Residue "A ARG 255": "NH1" <-> "NH2" Residue "A ARG 284": "NH1" <-> "NH2" Residue "A GLU 331": "OE1" <-> "OE2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A ARG 364": "NH1" <-> "NH2" Residue "A ARG 439": "NH1" <-> "NH2" Residue "A ARG 458": "NH1" <-> "NH2" Residue "A ARG 483": "NH1" <-> "NH2" Residue "A ARG 504": "NH1" <-> "NH2" Residue "A GLU 514": "OE1" <-> "OE2" Residue "A ARG 546": "NH1" <-> "NH2" Residue "A ARG 549": "NH1" <-> "NH2" Residue "A ARG 578": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 4513 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 4313 Classifications: {'peptide': 535} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 515} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 3 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: "E" 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: "F" 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: 6 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 17 Unusual residues: {' CA': 2, ' ZN': 1, 'NAG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.19, per 1000 atoms: 0.71 Number of scatterers: 4513 At special positions: 0 Unit cell: (99.64, 81.62, 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 907 8.00 N 748 7.00 C 2834 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 107 " - pdb=" SG CYS A 259 " distance=2.03 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 147 " distance=2.03 Simple disulfide: pdb=" SG CYS A 269 " - pdb=" SG CYS A 277 " distance=2.03 Simple disulfide: pdb=" SG CYS A 343 " - pdb=" SG CYS A 431 " distance=2.04 Simple disulfide: pdb=" SG CYS A 557 " - pdb=" SG CYS A 559 " distance=2.05 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 B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " BETA1-6 " NAG F 1 " - " FUC F 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A 704 " - " ASN A 539 " " NAG B 1 " - " ASN A 140 " " NAG C 1 " - " ASN A 258 " " NAG D 1 " - " ASN A 222 " " NAG E 1 " - " ASN A 440 " " NAG F 1 " - " ASN A 414 " Time building additional restraints: 2.17 Conformation dependent library (CDL) restraints added in 763.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 702 " pdb="ZN ZN A 702 " - pdb=" NE2 HIS A 165 " pdb="ZN ZN A 702 " - pdb=" NE2 HIS A 155 " pdb="ZN ZN A 702 " - pdb=" NE2 HIS A 159 " 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 998 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 10 sheets defined 23.6% alpha, 28.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 88 through 106 Processing helix chain 'A' and resid 149 through 162 Processing helix chain 'A' and resid 165 through 169 Processing helix chain 'A' and resid 171 through 174 Processing helix chain 'A' and resid 180 through 183 Processing helix chain 'A' and resid 187 through 192 Processing helix chain 'A' and resid 232 through 238 Processing helix chain 'A' and resid 246 through 258 Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 411 through 415 Processing helix chain 'A' and resid 440 through 448 removed outlier: 4.317A pdb=" N GLU A 446 " --> pdb=" O SER A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 497 Processing helix chain 'A' and resid 516 through 520 Processing helix chain 'A' and resid 535 through 539 Processing helix chain 'A' and resid 546 through 551 Processing helix chain 'A' and resid 573 through 577 Processing helix chain 'A' and resid 597 through 600 Processing sheet with id=AA1, first strand: chain 'A' and resid 67 through 68 Processing sheet with id=AA2, first strand: chain 'A' and resid 110 through 112 removed outlier: 7.977A pdb=" N PHE A 122 " --> pdb=" O PRO A 80 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE A 82 " --> pdb=" O PHE A 122 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ILE A 121 " --> pdb=" O ILE A 141 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 178 Processing sheet with id=AA4, first strand: chain 'A' and resid 265 through 269 Processing sheet with id=AA5, first strand: chain 'A' and resid 265 through 269 removed outlier: 5.726A pdb=" N LEU A 421 " --> pdb=" O LYS A 349 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N LYS A 349 " --> pdb=" O LEU A 421 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N ASP A 423 " --> pdb=" O PHE A 347 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N PHE A 347 " --> pdb=" O ASP A 423 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 280 through 281 removed outlier: 6.790A pdb=" N LEU A 358 " --> pdb=" O THR A 379 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N THR A 379 " --> pdb=" O LEU A 358 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL A 360 " --> pdb=" O VAL A 377 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 434 through 438 Processing sheet with id=AA8, first strand: chain 'A' and resid 454 through 455 Processing sheet with id=AA9, first strand: chain 'A' and resid 454 through 455 removed outlier: 3.951A pdb=" N GLY A 466 " --> pdb=" O CYS A 489 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU A 482 " --> pdb=" O GLY A 569 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 552 through 553 158 hydrogen bonds defined for protein. 354 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: 1.41 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: 1.21 - 1.33: 1084 1.33 - 1.45: 1057 1.45 - 1.57: 2449 1.57 - 1.69: 0 1.69 - 1.81: 30 Bond restraints: 4620 Sorted by residual: bond pdb=" CZ ARG A 169 " pdb=" NH2 ARG A 169 " ideal model delta sigma weight residual 1.330 1.289 0.041 1.30e-02 5.92e+03 1.01e+01 bond pdb=" CZ ARG A 172 " pdb=" NH2 ARG A 172 " ideal model delta sigma weight residual 1.330 1.289 0.041 1.30e-02 5.92e+03 9.92e+00 bond pdb=" N VAL A 371 " pdb=" CA VAL A 371 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.71e+00 bond pdb=" CZ ARG A 518 " pdb=" NH2 ARG A 518 " ideal model delta sigma weight residual 1.330 1.292 0.038 1.30e-02 5.92e+03 8.58e+00 bond pdb=" CZ ARG A 103 " pdb=" NH2 ARG A 103 " ideal model delta sigma weight residual 1.330 1.292 0.038 1.30e-02 5.92e+03 8.47e+00 ... (remaining 4615 not shown) Histogram of bond angle deviations from ideal: 97.33 - 104.87: 70 104.87 - 112.40: 2083 112.40 - 119.94: 1989 119.94 - 127.47: 2086 127.47 - 135.01: 43 Bond angle restraints: 6271 Sorted by residual: angle pdb=" CA PHE A 590 " pdb=" CB PHE A 590 " pdb=" CG PHE A 590 " ideal model delta sigma weight residual 113.80 118.92 -5.12 1.00e+00 1.00e+00 2.62e+01 angle pdb=" CA ASP A 564 " pdb=" CB ASP A 564 " pdb=" CG ASP A 564 " ideal model delta sigma weight residual 112.60 117.67 -5.07 1.00e+00 1.00e+00 2.57e+01 angle pdb=" N TYR A 113 " pdb=" CA TYR A 113 " pdb=" C TYR A 113 " ideal model delta sigma weight residual 111.07 116.26 -5.19 1.07e+00 8.73e-01 2.35e+01 angle pdb=" CB HIS A 573 " pdb=" CG HIS A 573 " pdb=" CD2 HIS A 573 " ideal model delta sigma weight residual 131.20 124.97 6.23 1.30e+00 5.92e-01 2.30e+01 angle pdb=" OE1 GLN A 345 " pdb=" CD GLN A 345 " pdb=" NE2 GLN A 345 " ideal model delta sigma weight residual 122.60 117.87 4.73 1.00e+00 1.00e+00 2.23e+01 ... (remaining 6266 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.01: 2642 18.01 - 36.03: 159 36.03 - 54.04: 23 54.04 - 72.05: 14 72.05 - 90.06: 2 Dihedral angle restraints: 2840 sinusoidal: 1285 harmonic: 1555 Sorted by residual: dihedral pdb=" CB CYS A 128 " pdb=" SG CYS A 128 " pdb=" SG CYS A 147 " pdb=" CB CYS A 147 " ideal model delta sinusoidal sigma weight residual 93.00 -176.94 -90.06 1 1.00e+01 1.00e-02 9.61e+01 dihedral pdb=" CB CYS A 557 " pdb=" SG CYS A 557 " pdb=" SG CYS A 559 " pdb=" CB CYS A 559 " ideal model delta sinusoidal sigma weight residual -86.00 -139.17 53.17 1 1.00e+01 1.00e-02 3.84e+01 dihedral pdb=" CA TRP A 567 " pdb=" C TRP A 567 " pdb=" N SER A 568 " pdb=" CA SER A 568 " ideal model delta harmonic sigma weight residual 180.00 150.29 29.71 0 5.00e+00 4.00e-02 3.53e+01 ... (remaining 2837 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 398 0.079 - 0.157: 236 0.157 - 0.236: 62 0.236 - 0.314: 14 0.314 - 0.393: 4 Chirality restraints: 714 Sorted by residual: 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 -2.12 -0.28 2.00e-02 2.50e+03 1.93e+02 chirality pdb=" C1 BMA C 3 " pdb=" O4 NAG C 2 " pdb=" C2 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-02 2.50e+03 6.44e+01 chirality pdb=" C1 FUC F 4 " pdb=" O6 NAG F 1 " pdb=" C2 FUC F 4 " pdb=" O5 FUC F 4 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-02 2.50e+03 4.73e+01 ... (remaining 711 not shown) Planarity restraints: 803 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 1 " -0.314 2.00e-02 2.50e+03 2.72e-01 9.25e+02 pdb=" C7 NAG C 1 " 0.070 2.00e-02 2.50e+03 pdb=" C8 NAG C 1 " -0.027 2.00e-02 2.50e+03 pdb=" N2 NAG C 1 " 0.474 2.00e-02 2.50e+03 pdb=" O7 NAG C 1 " -0.202 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " -0.205 2.00e-02 2.50e+03 1.68e-01 3.55e+02 pdb=" C7 NAG D 1 " 0.056 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " -0.148 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " 0.273 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 704 " 0.183 2.00e-02 2.50e+03 1.51e-01 2.85e+02 pdb=" C7 NAG A 704 " -0.051 2.00e-02 2.50e+03 pdb=" C8 NAG A 704 " 0.134 2.00e-02 2.50e+03 pdb=" N2 NAG A 704 " -0.245 2.00e-02 2.50e+03 pdb=" O7 NAG A 704 " -0.021 2.00e-02 2.50e+03 ... (remaining 800 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 823 2.81 - 3.33: 4208 3.33 - 3.85: 7306 3.85 - 4.38: 9238 4.38 - 4.90: 15059 Nonbonded interactions: 36634 Sorted by model distance: nonbonded pdb=" OD1 ASP A 288 " pdb="CA CA A 701 " model vdw 2.282 2.510 nonbonded pdb=" OE2 GLU A 272 " pdb="CA CA A 703 " model vdw 2.302 2.510 nonbonded pdb=" O TYR A 313 " pdb="CA CA A 703 " model vdw 2.329 2.510 nonbonded pdb=" OD1 ASP A 285 " pdb="CA CA A 701 " model vdw 2.329 2.510 nonbonded pdb=" OD2 ASP A 285 " pdb="CA CA A 701 " model vdw 2.379 2.510 ... (remaining 36629 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 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' } 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: 0.010 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: 2.510 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 18.020 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:11.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 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 0.041 4620 Z= 0.754 Angle : 1.756 9.028 6271 Z= 1.171 Chirality : 0.102 0.393 714 Planarity : 0.020 0.272 797 Dihedral : 12.175 82.604 1827 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 0.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Cbeta Deviations : 0.40 % Peptide Plane: Cis-proline : 10.53 % 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: -0.18 (0.34), residues: 533 helix: -0.97 (0.58), residues: 62 sheet: 0.51 (0.43), residues: 131 loop : -0.13 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.016 TRP A 544 HIS 0.012 0.003 HIS A 573 PHE 0.067 0.011 PHE A 593 TYR 0.104 0.020 TYR A 313 ARG 0.009 0.001 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 0.558 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 1.3641 time to fit residues: 166.7096 Evaluate side-chains 76 residues out of total 477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.526 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 44 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN A 461 ASN A 474 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4620 Z= 0.241 Angle : 0.657 9.928 6271 Z= 0.350 Chirality : 0.046 0.209 714 Planarity : 0.004 0.026 797 Dihedral : 5.913 27.272 816 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.68 % Allowed : 11.55 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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 (0.34), residues: 533 helix: -0.26 (0.61), residues: 69 sheet: 0.48 (0.43), residues: 136 loop : -0.10 (0.32), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 361 HIS 0.008 0.001 HIS A 155 PHE 0.017 0.002 PHE A 245 TYR 0.010 0.001 TYR A 97 ARG 0.004 0.001 ARG A 549 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 77 time to evaluate : 0.581 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 82 average time/residue: 1.1620 time to fit residues: 99.2854 Evaluate side-chains 74 residues out of total 477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 70 time to evaluate : 0.552 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 2 residues processed: 2 average time/residue: 0.7581 time to fit residues: 2.2126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 26 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4620 Z= 0.261 Angle : 0.590 9.675 6271 Z= 0.312 Chirality : 0.045 0.202 714 Planarity : 0.004 0.029 797 Dihedral : 5.203 26.262 816 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.31 % Allowed : 14.50 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -0.00 (0.35), residues: 533 helix: 0.10 (0.64), residues: 69 sheet: 0.34 (0.43), residues: 140 loop : -0.10 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 361 HIS 0.007 0.001 HIS A 155 PHE 0.013 0.002 PHE A 593 TYR 0.017 0.001 TYR A 97 ARG 0.003 0.000 ARG A 549 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 67 time to evaluate : 0.557 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 71 average time/residue: 1.1829 time to fit residues: 87.4897 Evaluate side-chains 72 residues out of total 477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 68 time to evaluate : 0.537 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 2 average time/residue: 0.1074 time to fit residues: 0.9971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 47 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 HIS A 455 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 4620 Z= 0.314 Angle : 0.607 10.265 6271 Z= 0.318 Chirality : 0.045 0.205 714 Planarity : 0.004 0.031 797 Dihedral : 5.114 27.504 816 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.31 % Allowed : 14.50 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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 (0.35), residues: 533 helix: 0.27 (0.64), residues: 69 sheet: 0.37 (0.43), residues: 140 loop : -0.17 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 361 HIS 0.007 0.001 HIS A 155 PHE 0.013 0.002 PHE A 527 TYR 0.019 0.001 TYR A 97 ARG 0.003 0.000 ARG A 578 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 70 time to evaluate : 0.490 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 77 average time/residue: 1.2095 time to fit residues: 96.8626 Evaluate side-chains 75 residues out of total 477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 70 time to evaluate : 0.535 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 3 residues processed: 2 average time/residue: 0.0463 time to fit residues: 0.8646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 455 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.037 4620 Z= 0.451 Angle : 0.647 10.779 6271 Z= 0.335 Chirality : 0.048 0.204 714 Planarity : 0.004 0.034 797 Dihedral : 5.285 31.098 816 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.94 % Allowed : 15.55 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -0.23 (0.35), residues: 533 helix: 0.26 (0.64), residues: 69 sheet: 0.21 (0.41), residues: 153 loop : -0.38 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 361 HIS 0.008 0.002 HIS A 155 PHE 0.014 0.002 PHE A 486 TYR 0.021 0.002 TYR A 97 ARG 0.005 0.001 ARG A 255 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 71 time to evaluate : 0.557 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 5 residues processed: 79 average time/residue: 1.0645 time to fit residues: 87.8672 Evaluate side-chains 72 residues out of total 477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 67 time to evaluate : 0.476 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 3 residues processed: 2 average time/residue: 0.0418 time to fit residues: 0.7860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 10 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 455 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4620 Z= 0.218 Angle : 0.595 12.606 6271 Z= 0.311 Chirality : 0.044 0.218 714 Planarity : 0.003 0.029 797 Dihedral : 4.993 28.658 816 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.52 % Allowed : 17.65 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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 (0.35), residues: 533 helix: 0.69 (0.66), residues: 66 sheet: 0.39 (0.43), residues: 148 loop : -0.36 (0.33), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 129 HIS 0.007 0.001 HIS A 155 PHE 0.011 0.001 PHE A 486 TYR 0.019 0.001 TYR A 97 ARG 0.002 0.000 ARG A 255 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 71 time to evaluate : 0.545 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 81 average time/residue: 1.0729 time to fit residues: 90.7333 Evaluate side-chains 78 residues out of total 477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 70 time to evaluate : 0.550 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 7 residues processed: 1 average time/residue: 0.0458 time to fit residues: 0.7989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 51 optimal weight: 0.3980 chunk 31 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 20 optimal weight: 0.0980 chunk 30 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 455 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4620 Z= 0.192 Angle : 0.584 9.426 6271 Z= 0.305 Chirality : 0.044 0.157 714 Planarity : 0.003 0.029 797 Dihedral : 4.850 29.225 816 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.52 % Allowed : 18.49 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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 (0.36), residues: 533 helix: 0.79 (0.66), residues: 66 sheet: 0.49 (0.43), residues: 148 loop : -0.35 (0.34), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 129 HIS 0.007 0.001 HIS A 155 PHE 0.011 0.001 PHE A 486 TYR 0.008 0.001 TYR A 257 ARG 0.002 0.000 ARG A 578 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 74 time to evaluate : 0.552 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 83 average time/residue: 1.1029 time to fit residues: 95.4359 Evaluate side-chains 81 residues out of total 477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 74 time to evaluate : 0.538 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 1 average time/residue: 0.0459 time to fit residues: 0.7842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 9 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 25 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 48 optimal weight: 0.4980 chunk 44 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 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 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4620 Z= 0.214 Angle : 0.588 6.803 6271 Z= 0.310 Chirality : 0.044 0.177 714 Planarity : 0.003 0.031 797 Dihedral : 4.777 30.007 816 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.52 % Allowed : 19.12 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 533 helix: 0.91 (0.66), residues: 66 sheet: 0.53 (0.44), residues: 148 loop : -0.36 (0.33), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 129 HIS 0.007 0.001 HIS A 155 PHE 0.011 0.001 PHE A 486 TYR 0.022 0.001 TYR A 97 ARG 0.004 0.000 ARG A 284 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 74 time to evaluate : 0.542 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 84 average time/residue: 1.0765 time to fit residues: 94.4722 Evaluate side-chains 77 residues out of total 477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 70 time to evaluate : 0.562 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 1 average time/residue: 0.0434 time to fit residues: 0.8054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 20 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4620 Z= 0.238 Angle : 0.605 7.229 6271 Z= 0.322 Chirality : 0.045 0.179 714 Planarity : 0.003 0.031 797 Dihedral : 4.787 31.063 816 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.10 % Allowed : 19.75 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 0.00 (0.36), residues: 533 helix: 0.63 (0.65), residues: 69 sheet: 0.59 (0.44), residues: 147 loop : -0.39 (0.34), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 129 HIS 0.007 0.001 HIS A 155 PHE 0.011 0.001 PHE A 486 TYR 0.008 0.001 TYR A 97 ARG 0.004 0.000 ARG A 284 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 73 time to evaluate : 0.559 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 81 average time/residue: 1.1390 time to fit residues: 96.1593 Evaluate side-chains 78 residues out of total 477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 71 time to evaluate : 0.540 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 1 average time/residue: 0.0455 time to fit residues: 0.7981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 52 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4620 Z= 0.247 Angle : 0.641 8.719 6271 Z= 0.338 Chirality : 0.046 0.188 714 Planarity : 0.003 0.032 797 Dihedral : 4.880 31.930 816 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.89 % Allowed : 19.96 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 0.02 (0.36), residues: 533 helix: 0.94 (0.66), residues: 66 sheet: 0.60 (0.44), residues: 147 loop : -0.44 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 361 HIS 0.007 0.001 HIS A 155 PHE 0.012 0.001 PHE A 486 TYR 0.032 0.001 TYR A 97 ARG 0.003 0.000 ARG A 255 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 69 time to evaluate : 0.572 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 76 average time/residue: 1.1459 time to fit residues: 90.9263 Evaluate side-chains 75 residues out of total 477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 68 time to evaluate : 0.550 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 7 residues processed: 1 average time/residue: 0.1995 time to fit residues: 0.9656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 11 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 43 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 2 optimal weight: 0.0470 chunk 30 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.085319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.076262 restraints weight = 7808.216| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.16 r_work: 0.3049 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.3733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4620 Z= 0.201 Angle : 0.628 7.835 6271 Z= 0.331 Chirality : 0.045 0.190 714 Planarity : 0.003 0.030 797 Dihedral : 4.739 31.708 816 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 1.68 % Allowed : 20.59 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 533 helix: 0.96 (0.66), residues: 66 sheet: 0.66 (0.45), residues: 147 loop : -0.44 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 129 HIS 0.007 0.001 HIS A 155 PHE 0.011 0.001 PHE A 486 TYR 0.009 0.001 TYR A 97 ARG 0.003 0.000 ARG A 284 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2211.64 seconds wall clock time: 39 minutes 56.57 seconds (2396.57 seconds total)