Starting phenix.real_space_refine (version: dev) on Fri Feb 17 13:20:30 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upx_26677/02_2023/7upx_26677.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upx_26677/02_2023/7upx_26677.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upx_26677/02_2023/7upx_26677.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upx_26677/02_2023/7upx_26677.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upx_26677/02_2023/7upx_26677.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upx_26677/02_2023/7upx_26677.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.018 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 Process input model Symmetric amino acids flipped Residue "A TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 389": "OD1" <-> "OD2" Residue "A TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 398": "OD1" <-> "OD2" Residue "A ASP 427": "OD1" <-> "OD2" Residue "A GLU 465": "OE1" <-> "OE2" Residue "A TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 85": "OD1" <-> "OD2" Residue "H PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 129": "NH1" <-> "NH2" Residue "H PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 28": "OD1" <-> "OD2" Residue "L ASP 31": "OD1" <-> "OD2" Residue "L ASP 70": "OD1" <-> "OD2" Residue "L GLU 81": "OE1" <-> "OE2" Residue "L PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 143": "OE1" <-> "OE2" Residue "L GLU 161": "OE1" <-> "OE2" Residue "L ASP 167": "OD1" <-> "OD2" Residue "L ASP 170": "OD1" <-> "OD2" Residue "L TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 213": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 4930 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1569 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 11, 'TRANS': 186} Chain: "H" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1701 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 213} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1622 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 200} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "B" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.32, per 1000 atoms: 0.67 Number of scatterers: 4930 At special positions: 0 Unit cell: (96.28, 82.17, 110.39, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 20 16.00 O 977 8.00 N 821 7.00 C 3112 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS H 140 " - pdb=" SG CYS H 196 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " 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 B 1 " - " NAG B 2 " BETA1-6 " NAG B 1 " - " FUC B 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG B 1 " - " ASN A 343 " Time building additional restraints: 2.09 Conformation dependent library (CDL) restraints added in 761.9 milliseconds 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1172 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 13 sheets defined 12.1% alpha, 35.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.072A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.579A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 removed outlier: 4.232A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA A 411 " --> pdb=" O ARG A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 156 through 158 No H-bonds generated for 'chain 'H' and resid 156 through 158' Processing helix chain 'H' and resid 187 through 191 removed outlier: 3.990A pdb=" N GLY H 190 " --> pdb=" O SER H 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 201 through 204 Processing helix chain 'L' and resid 121 through 127 Processing helix chain 'L' and resid 183 through 188 removed outlier: 3.652A pdb=" N GLU L 187 " --> pdb=" O LYS L 183 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS L 188 " --> pdb=" O ALA L 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 183 through 188' Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.513A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.877A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.524A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 120 through 124 removed outlier: 5.965A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 120 through 124 removed outlier: 5.965A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 151 through 154 removed outlier: 4.205A pdb=" N TYR H 194 " --> pdb=" O VAL H 211 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 4 through 6 removed outlier: 4.317A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER L 67 " --> pdb=" O ASP L 70 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.264A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 114 through 118 removed outlier: 6.411A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 153 through 154 188 hydrogen bonds defined for protein. 456 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: 1.72 Time building geometry restraints manager: 2.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 819 1.30 - 1.43: 1420 1.43 - 1.56: 2788 1.56 - 1.69: 1 1.69 - 1.82: 23 Bond restraints: 5051 Sorted by residual: bond pdb=" C6 NAG B 1 " pdb=" O6 NAG B 1 " ideal model delta sigma weight residual 1.421 1.478 -0.057 1.00e-02 1.00e+04 3.28e+01 bond pdb=" C TYR H 145 " pdb=" O TYR H 145 " ideal model delta sigma weight residual 1.235 1.174 0.061 1.22e-02 6.72e+03 2.49e+01 bond pdb=" C4 NAG B 1 " pdb=" O4 NAG B 1 " ideal model delta sigma weight residual 1.423 1.470 -0.047 1.00e-02 1.00e+04 2.21e+01 bond pdb=" C5 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.435 1.482 -0.047 1.10e-02 8.26e+03 1.85e+01 bond pdb=" CA ARG A 466 " pdb=" C ARG A 466 " ideal model delta sigma weight residual 1.520 1.566 -0.046 1.20e-02 6.94e+03 1.45e+01 ... (remaining 5046 not shown) Histogram of bond angle deviations from ideal: 99.65 - 106.87: 235 106.87 - 114.09: 2569 114.09 - 121.31: 2629 121.31 - 128.52: 1415 128.52 - 135.74: 30 Bond angle restraints: 6878 Sorted by residual: angle pdb=" C GLU H 148 " pdb=" N PRO H 149 " pdb=" CA PRO H 149 " ideal model delta sigma weight residual 119.84 133.01 -13.17 1.25e+00 6.40e-01 1.11e+02 angle pdb=" N PHE H 146 " pdb=" CA PHE H 146 " pdb=" C PHE H 146 " ideal model delta sigma weight residual 109.81 123.29 -13.48 2.21e+00 2.05e-01 3.72e+01 angle pdb=" CA PHE H 100G" pdb=" CB PHE H 100G" pdb=" CG PHE H 100G" ideal model delta sigma weight residual 113.80 119.88 -6.08 1.00e+00 1.00e+00 3.70e+01 angle pdb=" C ARG H 82B" pdb=" N LEU H 82C" pdb=" CA LEU H 82C" ideal model delta sigma weight residual 121.05 129.71 -8.66 1.43e+00 4.89e-01 3.67e+01 angle pdb=" CA ASN A 422 " pdb=" CB ASN A 422 " pdb=" CG ASN A 422 " ideal model delta sigma weight residual 112.60 118.47 -5.87 1.00e+00 1.00e+00 3.45e+01 ... (remaining 6873 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.12: 2733 17.12 - 34.24: 192 34.24 - 51.36: 38 51.36 - 68.47: 12 68.47 - 85.59: 8 Dihedral angle restraints: 2983 sinusoidal: 1144 harmonic: 1839 Sorted by residual: dihedral pdb=" C TYR A 495 " pdb=" N TYR A 495 " pdb=" CA TYR A 495 " pdb=" CB TYR A 495 " ideal model delta harmonic sigma weight residual -122.60 -108.66 -13.94 0 2.50e+00 1.60e-01 3.11e+01 dihedral pdb=" N TYR L 140 " pdb=" C TYR L 140 " pdb=" CA TYR L 140 " pdb=" CB TYR L 140 " ideal model delta harmonic sigma weight residual 122.80 135.52 -12.72 0 2.50e+00 1.60e-01 2.59e+01 dihedral pdb=" CA TYR H 91 " pdb=" C TYR H 91 " pdb=" N CYS H 92 " pdb=" CA CYS H 92 " ideal model delta harmonic sigma weight residual 180.00 155.31 24.69 0 5.00e+00 4.00e-02 2.44e+01 ... (remaining 2980 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 597 0.120 - 0.239: 146 0.239 - 0.358: 21 0.358 - 0.477: 4 0.477 - 0.596: 1 Chirality restraints: 769 Sorted by residual: chirality pdb=" C1 FUC B 3 " pdb=" O6 NAG B 1 " pdb=" C2 FUC B 3 " pdb=" O5 FUC B 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-02 2.50e+03 5.22e+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 -2.54 0.14 2.00e-02 2.50e+03 4.89e+01 chirality pdb=" CA TYR L 140 " pdb=" N TYR L 140 " pdb=" C TYR L 140 " pdb=" CB TYR L 140 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 8.89e+00 ... (remaining 766 not shown) Planarity restraints: 886 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR L 32 " -0.100 2.00e-02 2.50e+03 5.75e-02 6.62e+01 pdb=" CG TYR L 32 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR L 32 " 0.055 2.00e-02 2.50e+03 pdb=" CD2 TYR L 32 " 0.043 2.00e-02 2.50e+03 pdb=" CE1 TYR L 32 " 0.030 2.00e-02 2.50e+03 pdb=" CE2 TYR L 32 " 0.046 2.00e-02 2.50e+03 pdb=" CZ TYR L 32 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR L 32 " -0.091 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 90 " -0.075 2.00e-02 2.50e+03 4.78e-02 4.58e+01 pdb=" CG TYR H 90 " 0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR H 90 " 0.035 2.00e-02 2.50e+03 pdb=" CD2 TYR H 90 " 0.022 2.00e-02 2.50e+03 pdb=" CE1 TYR H 90 " 0.029 2.00e-02 2.50e+03 pdb=" CE2 TYR H 90 " 0.043 2.00e-02 2.50e+03 pdb=" CZ TYR H 90 " 0.022 2.00e-02 2.50e+03 pdb=" OH TYR H 90 " -0.088 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR L 91 " 0.093 2.00e-02 2.50e+03 4.74e-02 4.50e+01 pdb=" CG TYR L 91 " -0.057 2.00e-02 2.50e+03 pdb=" CD1 TYR L 91 " -0.043 2.00e-02 2.50e+03 pdb=" CD2 TYR L 91 " -0.049 2.00e-02 2.50e+03 pdb=" CE1 TYR L 91 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR L 91 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR L 91 " 0.026 2.00e-02 2.50e+03 pdb=" OH TYR L 91 " 0.034 2.00e-02 2.50e+03 ... (remaining 883 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 118 2.72 - 3.27: 4640 3.27 - 3.81: 7348 3.81 - 4.36: 10325 4.36 - 4.90: 16877 Nonbonded interactions: 39308 Sorted by model distance: nonbonded pdb=" OE2 GLU L 105 " pdb=" OH TYR L 140 " model vdw 2.176 2.440 nonbonded pdb=" CB GLU H 148 " pdb=" CD PRO H 149 " model vdw 2.190 3.840 nonbonded pdb=" OD1 ASP A 442 " pdb=" OG SER H 100B" model vdw 2.297 2.440 nonbonded pdb=" O ARG L 142 " pdb=" N ALA L 144 " model vdw 2.421 2.520 nonbonded pdb=" NZ LYS H 209 " pdb=" OE1 GLU L 123 " model vdw 2.429 2.520 ... (remaining 39303 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 3112 2.51 5 N 821 2.21 5 O 977 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 6.640 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: 24.420 Check model and map are aligned: 0.090 Process input model: 18.120 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.050 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 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 0.078 5051 Z= 0.807 Angle : 1.874 13.479 6878 Z= 1.231 Chirality : 0.105 0.596 769 Planarity : 0.012 0.120 885 Dihedral : 13.663 85.594 1799 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 1.43 % Allowed : 5.41 % Favored : 93.16 % Rotamer Outliers : 2.20 % Cbeta Deviations : 0.68 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.32), residues: 629 helix: -3.80 (0.43), residues: 46 sheet: 0.50 (0.33), residues: 235 loop : -0.57 (0.32), residues: 348 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 99 time to evaluate : 0.602 Fit side-chains outliers start: 12 outliers final: 5 residues processed: 109 average time/residue: 0.2324 time to fit residues: 31.0099 Evaluate side-chains 79 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 74 time to evaluate : 0.662 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0522 time to fit residues: 1.2119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 16 optimal weight: 0.0870 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 48 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN L 189 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 5051 Z= 0.265 Angle : 0.729 10.396 6878 Z= 0.380 Chirality : 0.049 0.181 769 Planarity : 0.005 0.039 885 Dihedral : 7.132 77.911 711 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.48 % Allowed : 3.66 % Favored : 95.87 % Rotamer Outliers : 1.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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 (0.34), residues: 629 helix: -2.88 (0.57), residues: 47 sheet: 0.81 (0.32), residues: 265 loop : -0.21 (0.36), residues: 317 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 93 time to evaluate : 0.590 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 98 average time/residue: 0.2628 time to fit residues: 30.9382 Evaluate side-chains 80 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 76 time to evaluate : 0.603 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0490 time to fit residues: 1.0439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 56 optimal weight: 10.0000 chunk 60 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 45 optimal weight: 0.0770 overall best weight: 1.1142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 422 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.046 5051 Z= 0.413 Angle : 0.743 9.628 6878 Z= 0.378 Chirality : 0.049 0.217 769 Planarity : 0.005 0.034 885 Dihedral : 6.851 79.109 711 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.25 % Favored : 94.44 % Rotamer Outliers : 1.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.34), residues: 629 helix: -2.77 (0.57), residues: 52 sheet: 0.74 (0.33), residues: 259 loop : -0.47 (0.35), residues: 318 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 71 time to evaluate : 0.675 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 79 average time/residue: 0.3049 time to fit residues: 29.0039 Evaluate side-chains 73 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 67 time to evaluate : 0.608 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1083 time to fit residues: 1.7670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 6 optimal weight: 0.4980 chunk 26 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 16 optimal weight: 0.4980 chunk 49 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN L 189 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 5051 Z= 0.250 Angle : 0.656 8.302 6878 Z= 0.334 Chirality : 0.046 0.169 769 Planarity : 0.004 0.032 885 Dihedral : 6.598 77.516 711 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.13 % Favored : 95.55 % Rotamer Outliers : 1.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.34), residues: 629 helix: -2.48 (0.60), residues: 52 sheet: 0.81 (0.32), residues: 259 loop : -0.38 (0.36), residues: 318 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 69 time to evaluate : 0.571 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 74 average time/residue: 0.2399 time to fit residues: 21.8730 Evaluate side-chains 67 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 64 time to evaluate : 0.518 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0469 time to fit residues: 1.0275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 41 optimal weight: 0.4980 chunk 30 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 15 optimal weight: 0.0670 chunk 20 optimal weight: 0.4980 chunk 11 optimal weight: 0.9980 overall best weight: 0.4918 ------------------------------------------------------------------------------- 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: 0.8772 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 5051 Z= 0.219 Angle : 0.628 7.664 6878 Z= 0.316 Chirality : 0.045 0.197 769 Planarity : 0.004 0.031 885 Dihedral : 6.406 77.144 711 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.97 % Favored : 95.71 % Rotamer Outliers : 1.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.34), residues: 629 helix: -1.85 (0.69), residues: 46 sheet: 0.90 (0.33), residues: 259 loop : -0.11 (0.36), residues: 324 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 67 time to evaluate : 0.591 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 71 average time/residue: 0.2389 time to fit residues: 20.9499 Evaluate side-chains 66 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 63 time to evaluate : 0.575 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0513 time to fit residues: 1.0637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 59 optimal weight: 6.9990 chunk 49 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 31 optimal weight: 0.2980 chunk 57 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.8787 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 5051 Z= 0.276 Angle : 0.644 7.773 6878 Z= 0.323 Chirality : 0.046 0.181 769 Planarity : 0.004 0.031 885 Dihedral : 6.390 77.088 711 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.29 % Favored : 95.39 % Rotamer Outliers : 0.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.35), residues: 629 helix: -1.65 (0.73), residues: 46 sheet: 0.92 (0.33), residues: 259 loop : -0.10 (0.37), residues: 324 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 65 time to evaluate : 0.594 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 66 average time/residue: 0.2538 time to fit residues: 20.5974 Evaluate side-chains 65 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 63 time to evaluate : 0.619 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0523 time to fit residues: 1.0029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 43 optimal weight: 0.9980 chunk 33 optimal weight: 10.0000 chunk 50 optimal weight: 0.0270 chunk 59 optimal weight: 5.9990 chunk 37 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 overall best weight: 0.6238 ------------------------------------------------------------------------------- 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: 0.8780 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 5051 Z= 0.250 Angle : 0.630 7.428 6878 Z= 0.315 Chirality : 0.045 0.176 769 Planarity : 0.004 0.030 885 Dihedral : 6.324 76.537 711 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.61 % Favored : 95.07 % Rotamer Outliers : 0.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.35), residues: 629 helix: -1.08 (0.84), residues: 40 sheet: 0.92 (0.32), residues: 265 loop : -0.18 (0.36), residues: 324 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 65 time to evaluate : 0.537 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 68 average time/residue: 0.2503 time to fit residues: 20.7743 Evaluate side-chains 66 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 63 time to evaluate : 0.596 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0503 time to fit residues: 1.2205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 52 optimal weight: 0.0000 chunk 55 optimal weight: 0.8980 chunk 33 optimal weight: 8.9990 overall best weight: 0.5584 ------------------------------------------------------------------------------- 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: 0.8773 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 5051 Z= 0.231 Angle : 0.618 7.205 6878 Z= 0.308 Chirality : 0.045 0.168 769 Planarity : 0.004 0.031 885 Dihedral : 6.250 76.416 711 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.97 % Favored : 95.87 % Rotamer Outliers : 0.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.35), residues: 629 helix: -1.12 (0.84), residues: 40 sheet: 1.03 (0.33), residues: 255 loop : -0.27 (0.35), residues: 334 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 66 time to evaluate : 0.537 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 68 average time/residue: 0.2514 time to fit residues: 20.9625 Evaluate side-chains 65 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 64 time to evaluate : 0.595 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0501 time to fit residues: 0.8894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 35 optimal weight: 0.0370 chunk 27 optimal weight: 0.0870 chunk 40 optimal weight: 1.9990 overall best weight: 0.5236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 199 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 5051 Z= 0.223 Angle : 0.617 7.349 6878 Z= 0.306 Chirality : 0.045 0.162 769 Planarity : 0.004 0.030 885 Dihedral : 6.213 76.024 711 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.29 % Favored : 95.55 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.35), residues: 629 helix: -1.12 (0.83), residues: 40 sheet: 1.02 (0.33), residues: 255 loop : -0.27 (0.36), residues: 334 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 66 time to evaluate : 0.472 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 67 average time/residue: 0.2703 time to fit residues: 21.8340 Evaluate side-chains 66 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.604 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 61 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 30 optimal weight: 0.4980 chunk 39 optimal weight: 3.9990 chunk 52 optimal weight: 0.0770 chunk 15 optimal weight: 0.9980 chunk 45 optimal weight: 0.3980 chunk 7 optimal weight: 0.7980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 199 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 5051 Z= 0.210 Angle : 0.611 7.402 6878 Z= 0.302 Chirality : 0.045 0.159 769 Planarity : 0.004 0.030 885 Dihedral : 6.144 75.758 711 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.13 % Favored : 95.71 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.34), residues: 629 helix: -1.10 (0.90), residues: 34 sheet: 0.98 (0.33), residues: 257 loop : -0.22 (0.35), residues: 338 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.588 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.2573 time to fit residues: 20.1947 Evaluate side-chains 64 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.581 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 0.2980 chunk 49 optimal weight: 0.9990 chunk 20 optimal weight: 0.3980 chunk 50 optimal weight: 0.3980 chunk 6 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 35 optimal weight: 0.0020 chunk 56 optimal weight: 7.9990 chunk 33 optimal weight: 9.9990 overall best weight: 0.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 199 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.149543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.108330 restraints weight = 6211.728| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.43 r_work: 0.3068 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 5051 Z= 0.189 Angle : 0.599 7.285 6878 Z= 0.296 Chirality : 0.044 0.154 769 Planarity : 0.004 0.030 885 Dihedral : 6.068 75.692 711 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.45 % Favored : 95.39 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.35), residues: 629 helix: -1.09 (0.89), residues: 34 sheet: 0.98 (0.33), residues: 257 loop : -0.19 (0.35), residues: 338 =============================================================================== Job complete usr+sys time: 1862.03 seconds wall clock time: 34 minutes 32.40 seconds (2072.40 seconds total)