Starting phenix.real_space_refine on Thu Dec 7 21:40:57 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upx_26677/12_2023/7upx_26677.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upx_26677/12_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_26677/12_2023/7upx_26677.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upx_26677/12_2023/7upx_26677.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upx_26677/12_2023/7upx_26677.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upx_26677/12_2023/7upx_26677.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.018 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 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. 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-1.21rc1-5172/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: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.36, per 1000 atoms: 0.68 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: 1.91 Conformation dependent library (CDL) restraints added in 926.8 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: 0.63 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: 1.48 Time building geometry restraints manager: 2.10 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=" 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=" C1 FUC B 3 " pdb=" O5 FUC B 3 " ideal model delta sigma weight residual 1.400 1.481 -0.081 2.00e-02 2.50e+03 1.64e+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 bond pdb=" C6 NAG B 1 " pdb=" O6 NAG B 1 " ideal model delta sigma weight residual 1.408 1.478 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" C5 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.413 1.482 -0.069 2.00e-02 2.50e+03 1.20e+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: 2757 17.12 - 34.24: 188 34.24 - 51.36: 38 51.36 - 68.47: 14 68.47 - 85.59: 7 Dihedral angle restraints: 3004 sinusoidal: 1165 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 3001 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 595 0.120 - 0.239: 147 0.239 - 0.358: 22 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 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: 4.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 22.480 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 18.260 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 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 : 0.013 0.081 5051 Z= 0.820 Angle : 1.877 13.479 6878 Z= 1.230 Chirality : 0.106 0.596 769 Planarity : 0.012 0.120 885 Dihedral : 13.522 85.594 1820 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 % Allowed : 4.77 % Favored : 93.03 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.016 TRP L 35 HIS 0.010 0.004 HIS L 198 PHE 0.063 0.014 PHE H 100G TYR 0.100 0.016 TYR L 32 ARG 0.007 0.001 ARG H 100A *********************** 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 : 0.596 Fit side-chains outliers start: 12 outliers final: 5 residues processed: 109 average time/residue: 0.2325 time to fit residues: 30.5453 Evaluate side-chains 79 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 74 time to evaluate : 0.504 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0487 time to fit residues: 1.2294 ------------------------------------------------------------------------------- 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 A 450 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 5051 Z= 0.260 Angle : 0.752 10.669 6878 Z= 0.394 Chirality : 0.050 0.189 769 Planarity : 0.005 0.041 885 Dihedral : 6.358 39.784 732 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.48 % Allowed : 3.82 % Favored : 95.71 % Rotamer: Outliers : 1.10 % Allowed : 9.91 % Favored : 88.99 % 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: -0.02 (0.34), residues: 629 helix: -2.96 (0.55), residues: 47 sheet: 0.86 (0.32), residues: 262 loop : -0.22 (0.36), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP H 50 HIS 0.005 0.002 HIS H 200 PHE 0.036 0.002 PHE H 146 TYR 0.025 0.002 TYR L 91 ARG 0.004 0.001 ARG L 108 *********************** 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 97 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 91 time to evaluate : 0.563 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 96 average time/residue: 0.2531 time to fit residues: 29.2770 Evaluate side-chains 78 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 74 time to evaluate : 0.532 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0591 time to fit residues: 1.1495 ------------------------------------------------------------------------------- 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: 0.5980 chunk 17 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 15 optimal weight: 0.0870 chunk 56 optimal weight: 9.9990 chunk 60 optimal weight: 6.9990 chunk 50 optimal weight: 0.0010 chunk 55 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 overall best weight: 0.4564 ------------------------------------------------------------------------------- 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: 0.8492 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5051 Z= 0.205 Angle : 0.656 8.674 6878 Z= 0.334 Chirality : 0.046 0.169 769 Planarity : 0.004 0.033 885 Dihedral : 5.726 36.367 732 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.93 % Favored : 94.75 % Rotamer: Outliers : 1.65 % Allowed : 11.56 % Favored : 86.79 % 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: 0.12 (0.34), residues: 629 helix: -2.40 (0.64), residues: 46 sheet: 0.85 (0.33), residues: 259 loop : -0.10 (0.36), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 50 HIS 0.006 0.002 HIS H 35 PHE 0.016 0.002 PHE H 146 TYR 0.022 0.002 TYR L 91 ARG 0.003 0.000 ARG L 108 *********************** 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 87 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 78 time to evaluate : 0.580 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 83 average time/residue: 0.2788 time to fit residues: 27.4382 Evaluate side-chains 79 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 73 time to evaluate : 0.571 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0961 time to fit residues: 1.6086 ------------------------------------------------------------------------------- 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: 0.8980 chunk 6 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 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 394 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 5051 Z= 0.307 Angle : 0.679 8.559 6878 Z= 0.343 Chirality : 0.047 0.182 769 Planarity : 0.004 0.030 885 Dihedral : 5.705 37.871 732 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.29 % Favored : 95.39 % Rotamer: Outliers : 0.92 % Allowed : 13.39 % Favored : 85.69 % 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: 0.16 (0.34), residues: 629 helix: -2.09 (0.68), residues: 46 sheet: 0.88 (0.33), residues: 259 loop : -0.12 (0.36), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 50 HIS 0.006 0.002 HIS H 35 PHE 0.016 0.002 PHE H 146 TYR 0.023 0.002 TYR L 91 ARG 0.003 0.000 ARG L 108 *********************** 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 76 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 71 time to evaluate : 0.579 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 76 average time/residue: 0.2629 time to fit residues: 24.0934 Evaluate side-chains 69 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 67 time to evaluate : 0.591 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0538 time to fit residues: 1.0276 ------------------------------------------------------------------------------- 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: 0.9990 chunk 0 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 41 optimal weight: 0.0770 chunk 30 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 overall best weight: 0.6138 ------------------------------------------------------------------------------- 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: 0.8515 moved from start: 0.2903 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= 0.248 Angle : 0.642 7.935 6878 Z= 0.320 Chirality : 0.046 0.181 769 Planarity : 0.004 0.030 885 Dihedral : 5.578 38.352 732 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.13 % Favored : 95.55 % Rotamer: Outliers : 0.73 % Allowed : 13.94 % Favored : 85.32 % 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: 0.27 (0.34), residues: 629 helix: -1.93 (0.68), residues: 46 sheet: 0.97 (0.33), residues: 259 loop : -0.08 (0.36), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 50 HIS 0.005 0.001 HIS H 35 PHE 0.015 0.001 PHE H 146 TYR 0.020 0.002 TYR L 91 ARG 0.002 0.000 ARG L 108 *********************** 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 75 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 71 time to evaluate : 0.570 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 74 average time/residue: 0.2468 time to fit residues: 22.1239 Evaluate side-chains 69 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 66 time to evaluate : 0.553 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0489 time to fit residues: 1.0287 ------------------------------------------------------------------------------- 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: 0.6980 chunk 59 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 34 optimal weight: 0.0770 overall best weight: 0.6138 ------------------------------------------------------------------------------- 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: 0.8520 moved from start: 0.3039 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= 0.248 Angle : 0.635 7.585 6878 Z= 0.317 Chirality : 0.046 0.173 769 Planarity : 0.004 0.030 885 Dihedral : 5.491 39.069 732 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.29 % Favored : 95.39 % Rotamer: Outliers : 0.55 % Allowed : 15.23 % Favored : 84.22 % 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: -1.66 (0.72), residues: 46 sheet: 1.00 (0.33), residues: 259 loop : -0.06 (0.37), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 50 HIS 0.004 0.001 HIS H 35 PHE 0.013 0.001 PHE H 146 TYR 0.020 0.002 TYR L 91 ARG 0.005 0.000 ARG A 466 *********************** 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 69 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 66 time to evaluate : 0.563 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 68 average time/residue: 0.2480 time to fit residues: 20.6104 Evaluate side-chains 65 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 63 time to evaluate : 0.573 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0528 time to fit residues: 0.9806 ------------------------------------------------------------------------------- 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: 9.9990 chunk 50 optimal weight: 0.7980 chunk 59 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 36 optimal weight: 0.0670 chunk 27 optimal weight: 3.9990 chunk 23 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 overall best weight: 0.5518 ------------------------------------------------------------------------------- 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: 0.8512 moved from start: 0.3140 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= 0.227 Angle : 0.618 7.326 6878 Z= 0.310 Chirality : 0.045 0.167 769 Planarity : 0.004 0.030 885 Dihedral : 5.419 39.585 732 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.13 % Favored : 95.55 % Rotamer: Outliers : 0.92 % Allowed : 15.23 % Favored : 83.85 % 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: 0.36 (0.35), residues: 629 helix: -1.50 (0.75), residues: 46 sheet: 1.03 (0.33), residues: 259 loop : -0.09 (0.37), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 50 HIS 0.004 0.001 HIS H 35 PHE 0.012 0.001 PHE H 166 TYR 0.020 0.002 TYR L 91 ARG 0.003 0.000 ARG A 466 *********************** 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 71 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 66 time to evaluate : 0.559 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 68 average time/residue: 0.2504 time to fit residues: 20.7145 Evaluate side-chains 67 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 64 time to evaluate : 0.507 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0469 time to fit residues: 0.9323 ------------------------------------------------------------------------------- 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: 0.8980 chunk 40 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 5 optimal weight: 0.0870 chunk 46 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 57 optimal weight: 0.0040 chunk 52 optimal weight: 0.1980 chunk 55 optimal weight: 0.9980 chunk 33 optimal weight: 6.9990 overall best weight: 0.2970 ------------------------------------------------------------------------------- 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: 0.8474 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5051 Z= 0.158 Angle : 0.589 7.257 6878 Z= 0.293 Chirality : 0.044 0.158 769 Planarity : 0.004 0.030 885 Dihedral : 5.185 38.674 732 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.13 % Favored : 95.71 % Rotamer: Outliers : 0.18 % Allowed : 15.96 % Favored : 83.85 % 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: 0.46 (0.35), residues: 629 helix: -1.39 (0.75), residues: 46 sheet: 1.21 (0.33), residues: 254 loop : -0.12 (0.36), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 50 HIS 0.003 0.001 HIS H 35 PHE 0.010 0.001 PHE H 146 TYR 0.016 0.001 TYR L 91 ARG 0.003 0.000 ARG A 466 *********************** 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 70 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 69 time to evaluate : 0.618 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 70 average time/residue: 0.2526 time to fit residues: 21.4678 Evaluate side-chains 67 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 66 time to evaluate : 0.571 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0488 time to fit residues: 0.8754 ------------------------------------------------------------------------------- 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: 1.9990 chunk 43 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 50 optimal weight: 0.4980 chunk 52 optimal weight: 0.6980 chunk 55 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 ASN L 199 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5051 Z= 0.264 Angle : 0.632 7.408 6878 Z= 0.312 Chirality : 0.045 0.164 769 Planarity : 0.004 0.030 885 Dihedral : 5.363 40.730 732 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.77 % Favored : 95.07 % Rotamer: Outliers : 0.00 % Allowed : 17.06 % Favored : 82.94 % 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: 0.41 (0.35), residues: 629 helix: -1.06 (0.85), residues: 40 sheet: 1.20 (0.33), residues: 248 loop : -0.23 (0.35), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 50 HIS 0.004 0.001 HIS H 35 PHE 0.013 0.001 PHE L 71 TYR 0.022 0.002 TYR L 91 ARG 0.003 0.000 ARG A 466 *********************** 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: 0 poor density : 67 time to evaluate : 0.560 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.2675 time to fit residues: 21.8733 Evaluate side-chains 66 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.706 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7690 ------------------------------------------------------------------------------- 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: 0.9980 chunk 56 optimal weight: 0.4980 chunk 49 optimal weight: 0.9990 chunk 5 optimal weight: 0.0870 chunk 37 optimal weight: 0.9980 chunk 30 optimal weight: 0.0770 chunk 39 optimal weight: 3.9990 chunk 52 optimal weight: 0.0270 chunk 15 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 overall best weight: 0.2774 ------------------------------------------------------------------------------- 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: 0.8463 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5051 Z= 0.159 Angle : 0.582 7.527 6878 Z= 0.288 Chirality : 0.044 0.164 769 Planarity : 0.004 0.030 885 Dihedral : 5.117 39.268 732 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.66 % Favored : 96.18 % Rotamer: Outliers : 0.37 % Allowed : 16.88 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.35), residues: 629 helix: -1.01 (0.84), residues: 40 sheet: 1.15 (0.33), residues: 255 loop : -0.15 (0.36), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 50 HIS 0.003 0.001 HIS H 35 PHE 0.008 0.001 PHE H 166 TYR 0.014 0.001 TYR L 91 ARG 0.003 0.000 ARG A 466 ********************** 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 68 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 66 time to evaluate : 0.592 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 68 average time/residue: 0.2657 time to fit residues: 21.7377 Evaluate side-chains 66 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.513 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.8387 > 50: distance: 62 - 85: 16.765 distance: 69 - 97: 11.719 distance: 81 - 85: 15.148 distance: 85 - 86: 12.171 distance: 86 - 89: 21.522 distance: 87 - 88: 8.512 distance: 87 - 97: 4.747 distance: 89 - 90: 7.663 distance: 90 - 91: 21.298 distance: 90 - 92: 11.270 distance: 91 - 93: 9.274 distance: 92 - 94: 9.894 distance: 93 - 95: 12.750 distance: 94 - 95: 19.060 distance: 95 - 96: 16.249 distance: 97 - 98: 3.084 distance: 98 - 99: 3.945 distance: 98 - 101: 6.938 distance: 99 - 100: 14.680 distance: 101 - 102: 4.993 distance: 102 - 103: 3.533 distance: 102 - 104: 9.346 distance: 106 - 107: 5.845 distance: 106 - 109: 4.692 distance: 107 - 108: 5.877 distance: 107 - 117: 9.441 distance: 109 - 110: 7.172 distance: 110 - 111: 4.026 distance: 110 - 112: 3.864 distance: 111 - 113: 3.372 distance: 112 - 114: 3.831 distance: 115 - 116: 4.157 distance: 117 - 118: 5.259 distance: 118 - 119: 10.869 distance: 118 - 121: 6.467 distance: 119 - 120: 17.199 distance: 119 - 126: 15.655 distance: 122 - 123: 10.228 distance: 123 - 124: 8.204 distance: 124 - 125: 14.160 distance: 126 - 127: 6.169 distance: 127 - 128: 9.137 distance: 127 - 130: 12.469 distance: 128 - 129: 14.981 distance: 128 - 134: 10.042 distance: 130 - 131: 12.279 distance: 131 - 132: 28.117 distance: 131 - 133: 41.392 distance: 134 - 135: 5.855 distance: 134 - 140: 12.334 distance: 135 - 136: 17.462 distance: 135 - 138: 16.335 distance: 136 - 137: 19.509 distance: 136 - 141: 23.412 distance: 138 - 139: 6.819 distance: 139 - 140: 9.275 distance: 141 - 142: 16.344 distance: 142 - 143: 23.766 distance: 142 - 145: 16.286 distance: 143 - 144: 23.603 distance: 143 - 149: 16.880 distance: 145 - 146: 9.604 distance: 146 - 147: 20.582 distance: 146 - 148: 23.438 distance: 149 - 150: 21.143 distance: 150 - 151: 3.969 distance: 150 - 153: 18.098 distance: 151 - 152: 14.629 distance: 151 - 157: 6.608 distance: 153 - 154: 25.578 distance: 154 - 155: 4.782 distance: 154 - 156: 4.330 distance: 157 - 158: 5.324 distance: 158 - 159: 18.327 distance: 158 - 161: 18.873 distance: 159 - 160: 26.490 distance: 159 - 168: 9.434 distance: 161 - 162: 4.355 distance: 162 - 163: 13.761 distance: 162 - 164: 7.176 distance: 163 - 165: 16.755 distance: 164 - 166: 8.502 distance: 165 - 167: 12.860 distance: 166 - 167: 10.622 distance: 168 - 169: 10.306 distance: 169 - 172: 6.017 distance: 170 - 171: 4.958 distance: 170 - 175: 31.610 distance: 172 - 173: 14.953 distance: 172 - 174: 17.941