Starting phenix.real_space_refine on Fri Dec 8 04:18:40 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l47_0831/12_2023/6l47_0831_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l47_0831/12_2023/6l47_0831.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l47_0831/12_2023/6l47_0831_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l47_0831/12_2023/6l47_0831_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l47_0831/12_2023/6l47_0831_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l47_0831/12_2023/6l47_0831.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l47_0831/12_2023/6l47_0831.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l47_0831/12_2023/6l47_0831_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l47_0831/12_2023/6l47_0831_updated.pdb" } resolution = 3.5 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= 0.015 sd= 0.713 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 38 5.16 5 C 4796 2.51 5 N 1066 2.21 5 O 1100 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 7000 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3444 Classifications: {'peptide': 416} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 19, 'TRANS': 396} Chain breaks: 2 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 67 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 5, 'PHE:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 59 Chain: "B" Number of atoms: 3444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3444 Classifications: {'peptide': 416} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 19, 'TRANS': 396} Chain breaks: 2 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 67 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 5, 'PHE:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 59 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 1, 'E5L': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 1, 'E5L': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.21, per 1000 atoms: 0.60 Number of scatterers: 7000 At special positions: 0 Unit cell: (141.075, 86.735, 76.285, 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 38 16.00 O 1100 8.00 N 1066 7.00 C 4796 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 365 " - pdb=" SG CYS A 516 " distance=2.06 Simple disulfide: pdb=" SG CYS A 528 " - pdb=" SG CYS A 548 " distance=2.03 Simple disulfide: pdb=" SG CYS B 365 " - pdb=" SG CYS B 516 " distance=2.06 Simple disulfide: pdb=" SG CYS B 528 " - pdb=" SG CYS B 548 " distance=2.03 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 Time building additional restraints: 2.92 Conformation dependent library (CDL) restraints added in 1.3 seconds 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1604 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 28 helices and 0 sheets defined 71.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.34 Creating SS restraints... Processing helix chain 'A' and resid 128 through 134 removed outlier: 4.219A pdb=" N GLU A 134 " --> pdb=" O ASP A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 164 Processing helix chain 'A' and resid 173 through 177 Processing helix chain 'A' and resid 181 through 212 Proline residue: A 199 - end of helix Processing helix chain 'A' and resid 217 through 246 removed outlier: 3.870A pdb=" N GLY A 238 " --> pdb=" O VAL A 234 " (cutoff:3.500A) Proline residue: A 239 - end of helix removed outlier: 3.637A pdb=" N VAL A 243 " --> pdb=" O PRO A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 284 removed outlier: 3.676A pdb=" N PHE A 254 " --> pdb=" O PRO A 250 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE A 255 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE A 256 " --> pdb=" O SER A 252 " (cutoff:3.500A) Proline residue: A 276 - end of helix Processing helix chain 'A' and resid 294 through 302 removed outlier: 3.934A pdb=" N PHE A 302 " --> pdb=" O LEU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 345 removed outlier: 3.658A pdb=" N PHE A 335 " --> pdb=" O PHE A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 394 removed outlier: 4.306A pdb=" N ILE A 370 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N LEU A 371 " --> pdb=" O PHE A 367 " (cutoff:3.500A) Proline residue: A 372 - end of helix Processing helix chain 'A' and resid 413 through 418 Processing helix chain 'A' and resid 422 through 438 Processing helix chain 'A' and resid 446 through 466 removed outlier: 4.393A pdb=" N MET A 449 " --> pdb=" O SER A 446 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ALA A 451 " --> pdb=" O ALA A 448 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N PHE A 453 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N VAL A 466 " --> pdb=" O ALA A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 486 Processing helix chain 'A' and resid 498 through 527 Processing helix chain 'B' and resid 128 through 134 removed outlier: 4.219A pdb=" N GLU B 134 " --> pdb=" O ASP B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 164 Processing helix chain 'B' and resid 173 through 177 Processing helix chain 'B' and resid 181 through 212 Proline residue: B 199 - end of helix Processing helix chain 'B' and resid 217 through 246 removed outlier: 3.870A pdb=" N GLY B 238 " --> pdb=" O VAL B 234 " (cutoff:3.500A) Proline residue: B 239 - end of helix removed outlier: 3.636A pdb=" N VAL B 243 " --> pdb=" O PRO B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 284 removed outlier: 3.675A pdb=" N PHE B 254 " --> pdb=" O PRO B 250 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE B 255 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE B 256 " --> pdb=" O SER B 252 " (cutoff:3.500A) Proline residue: B 276 - end of helix Processing helix chain 'B' and resid 294 through 302 removed outlier: 3.934A pdb=" N PHE B 302 " --> pdb=" O LEU B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 345 removed outlier: 3.658A pdb=" N PHE B 335 " --> pdb=" O PHE B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 394 removed outlier: 4.306A pdb=" N ILE B 370 " --> pdb=" O VAL B 366 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N LEU B 371 " --> pdb=" O PHE B 367 " (cutoff:3.500A) Proline residue: B 372 - end of helix Processing helix chain 'B' and resid 413 through 418 Processing helix chain 'B' and resid 422 through 438 Processing helix chain 'B' and resid 446 through 466 removed outlier: 4.393A pdb=" N MET B 449 " --> pdb=" O SER B 446 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ALA B 451 " --> pdb=" O ALA B 448 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N PHE B 453 " --> pdb=" O LEU B 450 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N VAL B 466 " --> pdb=" O ALA B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 486 Processing helix chain 'B' and resid 498 through 527 430 hydrogen bonds defined for protein. 1206 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: 1.67 Time building geometry restraints manager: 3.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1940 1.34 - 1.46: 2208 1.46 - 1.58: 3064 1.58 - 1.70: 0 1.70 - 1.82: 60 Bond restraints: 7272 Sorted by residual: bond pdb=" N E5L B1001 " pdb=" C3 E5L B1001 " ideal model delta sigma weight residual 1.454 1.335 0.119 2.00e-02 2.50e+03 3.52e+01 bond pdb=" N E5L A1001 " pdb=" C3 E5L A1001 " ideal model delta sigma weight residual 1.454 1.335 0.119 2.00e-02 2.50e+03 3.52e+01 bond pdb=" N E5L A1001 " pdb=" C E5L A1001 " ideal model delta sigma weight residual 1.454 1.353 0.101 2.00e-02 2.50e+03 2.56e+01 bond pdb=" N E5L B1001 " pdb=" C E5L B1001 " ideal model delta sigma weight residual 1.454 1.353 0.101 2.00e-02 2.50e+03 2.56e+01 bond pdb=" C E5L B1001 " pdb=" C1 E5L B1001 " ideal model delta sigma weight residual 1.386 1.485 -0.099 2.00e-02 2.50e+03 2.45e+01 ... (remaining 7267 not shown) Histogram of bond angle deviations from ideal: 100.43 - 107.15: 247 107.15 - 113.88: 3904 113.88 - 120.60: 3225 120.60 - 127.32: 2450 127.32 - 134.04: 108 Bond angle restraints: 9934 Sorted by residual: angle pdb=" O E5L B1001 " pdb=" C1 E5L B1001 " pdb=" C6 E5L B1001 " ideal model delta sigma weight residual 103.61 120.64 -17.03 3.00e+00 1.11e-01 3.22e+01 angle pdb=" O E5L A1001 " pdb=" C1 E5L A1001 " pdb=" C6 E5L A1001 " ideal model delta sigma weight residual 103.61 120.63 -17.02 3.00e+00 1.11e-01 3.22e+01 angle pdb=" C E5L A1001 " pdb=" C1 E5L A1001 " pdb=" O E5L A1001 " ideal model delta sigma weight residual 136.26 120.75 15.51 3.00e+00 1.11e-01 2.67e+01 angle pdb=" C E5L B1001 " pdb=" C1 E5L B1001 " pdb=" O E5L B1001 " ideal model delta sigma weight residual 136.26 120.78 15.48 3.00e+00 1.11e-01 2.66e+01 angle pdb=" C HIS A 386 " pdb=" N CYS A 387 " pdb=" CA CYS A 387 " ideal model delta sigma weight residual 120.68 115.11 5.57 1.70e+00 3.46e-01 1.07e+01 ... (remaining 9929 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.28: 3970 26.28 - 52.55: 156 52.55 - 78.83: 12 78.83 - 105.10: 0 105.10 - 131.37: 8 Dihedral angle restraints: 4146 sinusoidal: 1660 harmonic: 2486 Sorted by residual: dihedral pdb=" CA ARG A 309 " pdb=" C ARG A 309 " pdb=" N ASP A 310 " pdb=" CA ASP A 310 " ideal model delta harmonic sigma weight residual 180.00 -158.38 -21.62 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA ARG B 309 " pdb=" C ARG B 309 " pdb=" N ASP B 310 " pdb=" CA ASP B 310 " ideal model delta harmonic sigma weight residual -180.00 -158.40 -21.60 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" C16 E5L A1001 " pdb=" C17 E5L A1001 " pdb=" C18 E5L A1001 " pdb=" C19 E5L A1001 " ideal model delta sinusoidal sigma weight residual 182.95 51.58 131.37 1 3.00e+01 1.11e-03 1.77e+01 ... (remaining 4143 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 890 0.057 - 0.115: 164 0.115 - 0.172: 12 0.172 - 0.230: 2 0.230 - 0.287: 2 Chirality restraints: 1070 Sorted by residual: chirality pdb=" C17 CLR A1002 " pdb=" C13 CLR A1002 " pdb=" C16 CLR A1002 " pdb=" C20 CLR A1002 " both_signs ideal model delta sigma weight residual False 2.55 2.27 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" C17 CLR B1002 " pdb=" C13 CLR B1002 " pdb=" C16 CLR B1002 " pdb=" C20 CLR B1002 " both_signs ideal model delta sigma weight residual False 2.55 2.27 0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" C20 CLR A1002 " pdb=" C17 CLR A1002 " pdb=" C21 CLR A1002 " pdb=" C22 CLR A1002 " both_signs ideal model delta sigma weight residual False 2.59 2.81 -0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 1067 not shown) Planarity restraints: 1180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N E5L A1001 " 0.201 2.00e-02 2.50e+03 1.26e-01 2.00e+02 pdb=" C E5L A1001 " -0.158 2.00e-02 2.50e+03 pdb=" C3 E5L A1001 " 0.045 2.00e-02 2.50e+03 pdb=" C4 E5L A1001 " -0.110 2.00e-02 2.50e+03 pdb=" O3 E5L A1001 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N E5L B1001 " -0.201 2.00e-02 2.50e+03 1.26e-01 2.00e+02 pdb=" C E5L B1001 " 0.157 2.00e-02 2.50e+03 pdb=" C3 E5L B1001 " -0.046 2.00e-02 2.50e+03 pdb=" C4 E5L B1001 " 0.110 2.00e-02 2.50e+03 pdb=" O3 E5L B1001 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 385 " -0.013 2.00e-02 2.50e+03 2.58e-02 6.67e+00 pdb=" C LEU B 385 " 0.045 2.00e-02 2.50e+03 pdb=" O LEU B 385 " -0.017 2.00e-02 2.50e+03 pdb=" N HIS B 386 " -0.015 2.00e-02 2.50e+03 ... (remaining 1177 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 1886 2.79 - 3.32: 6908 3.32 - 3.85: 11908 3.85 - 4.37: 12872 4.37 - 4.90: 21617 Nonbonded interactions: 55191 Sorted by model distance: nonbonded pdb=" OE1 GLU B 284 " pdb=" OG SER B 286 " model vdw 2.266 2.440 nonbonded pdb=" OE1 GLU A 284 " pdb=" OG SER A 286 " model vdw 2.266 2.440 nonbonded pdb=" O THR B 419 " pdb=" OG1 THR B 419 " model vdw 2.279 2.440 nonbonded pdb=" O THR A 419 " pdb=" OG1 THR A 419 " model vdw 2.279 2.440 nonbonded pdb=" O PRO A 216 " pdb=" N SER A 220 " model vdw 2.295 2.520 ... (remaining 55186 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.580 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: 0.010 Extract box with map and model: 2.130 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 22.400 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 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:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 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 : 0.005 0.119 7272 Z= 0.297 Angle : 0.819 17.025 9934 Z= 0.400 Chirality : 0.045 0.287 1070 Planarity : 0.008 0.126 1180 Dihedral : 14.765 131.375 2530 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.73 % Favored : 89.27 % Rotamer: Outliers : 3.34 % Allowed : 10.58 % Favored : 86.07 % 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: -3.09 (0.26), residues: 820 helix: -1.17 (0.19), residues: 586 sheet: None (None), residues: 0 loop : -4.15 (0.37), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 407 HIS 0.004 0.001 HIS A 425 PHE 0.020 0.002 PHE B 230 TYR 0.016 0.002 TYR A 308 ARG 0.003 0.000 ARG B 418 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 235 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 10 residues processed: 251 average time/residue: 0.2003 time to fit residues: 65.2146 Evaluate side-chains 176 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 166 time to evaluate : 0.784 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0673 time to fit residues: 2.2623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 41 optimal weight: 10.0000 chunk 33 optimal weight: 0.0970 chunk 64 optimal weight: 0.9990 chunk 24 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 chunk 47 optimal weight: 9.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 460 HIS B 460 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7272 Z= 0.195 Angle : 0.699 8.185 9934 Z= 0.355 Chirality : 0.041 0.160 1070 Planarity : 0.006 0.049 1180 Dihedral : 10.030 77.943 1072 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 5.01 % Allowed : 17.69 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.30), residues: 820 helix: -0.20 (0.21), residues: 592 sheet: None (None), residues: 0 loop : -3.36 (0.44), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 438 HIS 0.003 0.001 HIS A 143 PHE 0.028 0.002 PHE B 270 TYR 0.023 0.002 TYR A 308 ARG 0.006 0.001 ARG B 272 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 184 time to evaluate : 0.696 Fit side-chains revert: symmetry clash outliers start: 36 outliers final: 17 residues processed: 203 average time/residue: 0.1846 time to fit residues: 50.3648 Evaluate side-chains 169 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 152 time to evaluate : 0.781 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.0723 time to fit residues: 3.2237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 41 optimal weight: 10.0000 chunk 23 optimal weight: 0.0050 chunk 61 optimal weight: 4.9990 chunk 50 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 73 optimal weight: 8.9990 chunk 25 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 overall best weight: 2.3400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7272 Z= 0.243 Angle : 0.677 7.148 9934 Z= 0.352 Chirality : 0.042 0.166 1070 Planarity : 0.005 0.044 1180 Dihedral : 8.402 74.822 1072 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.51 % Favored : 90.49 % Rotamer: Outliers : 2.23 % Allowed : 22.84 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.30), residues: 820 helix: 0.35 (0.21), residues: 586 sheet: None (None), residues: 0 loop : -3.53 (0.42), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 438 HIS 0.005 0.001 HIS B 425 PHE 0.028 0.002 PHE A 270 TYR 0.028 0.002 TYR B 308 ARG 0.006 0.001 ARG A 272 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 164 time to evaluate : 0.785 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 7 residues processed: 173 average time/residue: 0.1695 time to fit residues: 40.5053 Evaluate side-chains 155 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 148 time to evaluate : 0.776 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0782 time to fit residues: 1.9721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 73 optimal weight: 7.9990 chunk 56 optimal weight: 0.4980 chunk 38 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 50 optimal weight: 0.0030 chunk 74 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 overall best weight: 0.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 329 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7272 Z= 0.184 Angle : 0.683 10.879 9934 Z= 0.338 Chirality : 0.041 0.162 1070 Planarity : 0.005 0.043 1180 Dihedral : 7.823 70.040 1072 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.27 % Favored : 90.73 % Rotamer: Outliers : 3.06 % Allowed : 22.98 % Favored : 73.96 % 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: -0.84 (0.30), residues: 820 helix: 0.51 (0.21), residues: 594 sheet: None (None), residues: 0 loop : -3.50 (0.43), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 438 HIS 0.002 0.001 HIS B 143 PHE 0.028 0.002 PHE A 227 TYR 0.023 0.002 TYR A 308 ARG 0.007 0.000 ARG B 418 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 167 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 13 residues processed: 178 average time/residue: 0.1668 time to fit residues: 40.7788 Evaluate side-chains 164 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 151 time to evaluate : 0.770 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0677 time to fit residues: 2.6137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 66 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 40 optimal weight: 9.9990 chunk 71 optimal weight: 7.9990 chunk 20 optimal weight: 9.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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: 0.7813 moved from start: 0.3803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7272 Z= 0.206 Angle : 0.669 9.962 9934 Z= 0.337 Chirality : 0.041 0.204 1070 Planarity : 0.006 0.058 1180 Dihedral : 7.705 74.492 1072 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.12 % Favored : 89.88 % Rotamer: Outliers : 1.67 % Allowed : 23.96 % Favored : 74.37 % 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: -0.65 (0.30), residues: 820 helix: 0.69 (0.21), residues: 596 sheet: None (None), residues: 0 loop : -3.60 (0.42), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 438 HIS 0.004 0.001 HIS B 425 PHE 0.033 0.002 PHE A 227 TYR 0.027 0.002 TYR B 336 ARG 0.005 0.000 ARG B 418 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 153 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 159 average time/residue: 0.1713 time to fit residues: 37.2923 Evaluate side-chains 154 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 149 time to evaluate : 0.765 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0678 time to fit residues: 1.6291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 26 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 46 optimal weight: 8.9990 chunk 19 optimal weight: 7.9990 chunk 79 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 36 optimal weight: 9.9990 chunk 6 optimal weight: 6.9990 chunk 41 optimal weight: 9.9990 chunk 76 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.3998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7272 Z= 0.209 Angle : 0.691 11.281 9934 Z= 0.342 Chirality : 0.042 0.187 1070 Planarity : 0.005 0.043 1180 Dihedral : 7.548 70.450 1072 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer: Outliers : 2.09 % Allowed : 23.96 % Favored : 73.96 % 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: -0.50 (0.31), residues: 820 helix: 0.84 (0.21), residues: 594 sheet: None (None), residues: 0 loop : -3.61 (0.42), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 438 HIS 0.003 0.001 HIS A 223 PHE 0.028 0.001 PHE B 270 TYR 0.028 0.002 TYR A 336 ARG 0.004 0.000 ARG B 418 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 163 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 7 residues processed: 171 average time/residue: 0.1829 time to fit residues: 41.8554 Evaluate side-chains 160 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 153 time to evaluate : 0.799 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0657 time to fit residues: 1.8953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 8 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 chunk 49 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.4211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7272 Z= 0.201 Angle : 0.698 10.267 9934 Z= 0.341 Chirality : 0.042 0.180 1070 Planarity : 0.005 0.043 1180 Dihedral : 7.496 73.326 1072 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.24 % Favored : 89.76 % Rotamer: Outliers : 1.39 % Allowed : 24.65 % Favored : 73.96 % 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: -0.51 (0.31), residues: 820 helix: 0.86 (0.22), residues: 594 sheet: None (None), residues: 0 loop : -3.71 (0.41), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 438 HIS 0.003 0.001 HIS A 223 PHE 0.030 0.001 PHE A 270 TYR 0.022 0.002 TYR B 322 ARG 0.009 0.000 ARG B 253 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 169 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 176 average time/residue: 0.1834 time to fit residues: 43.8588 Evaluate side-chains 156 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 152 time to evaluate : 0.818 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0725 time to fit residues: 1.5813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 23 optimal weight: 10.0000 chunk 15 optimal weight: 0.9990 chunk 50 optimal weight: 20.0000 chunk 53 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 71 optimal weight: 8.9990 chunk 75 optimal weight: 0.8980 chunk 69 optimal weight: 7.9990 chunk 73 optimal weight: 5.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.4400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7272 Z= 0.225 Angle : 0.753 11.598 9934 Z= 0.360 Chirality : 0.042 0.165 1070 Planarity : 0.005 0.042 1180 Dihedral : 7.464 70.905 1072 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.37 % Favored : 89.63 % Rotamer: Outliers : 0.42 % Allowed : 26.18 % Favored : 73.40 % 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: -0.45 (0.31), residues: 820 helix: 0.93 (0.22), residues: 592 sheet: None (None), residues: 0 loop : -3.73 (0.41), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 438 HIS 0.004 0.001 HIS A 223 PHE 0.028 0.001 PHE A 270 TYR 0.024 0.002 TYR B 322 ARG 0.004 0.000 ARG B 253 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 158 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 159 average time/residue: 0.1736 time to fit residues: 37.3888 Evaluate side-chains 152 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 150 time to evaluate : 0.750 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0784 time to fit residues: 1.2549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 75 optimal weight: 0.4980 chunk 44 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 69 optimal weight: 7.9990 chunk 73 optimal weight: 8.9990 chunk 48 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- 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: 0.7856 moved from start: 0.4460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7272 Z= 0.272 Angle : 0.767 12.565 9934 Z= 0.376 Chirality : 0.044 0.180 1070 Planarity : 0.005 0.045 1180 Dihedral : 7.618 71.190 1072 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.61 % Favored : 89.39 % Rotamer: Outliers : 0.56 % Allowed : 27.02 % Favored : 72.42 % 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: -0.53 (0.31), residues: 820 helix: 0.83 (0.21), residues: 606 sheet: None (None), residues: 0 loop : -3.92 (0.44), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 438 HIS 0.004 0.001 HIS A 425 PHE 0.029 0.002 PHE A 270 TYR 0.025 0.002 TYR B 308 ARG 0.004 0.000 ARG B 253 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 153 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 154 average time/residue: 0.1665 time to fit residues: 35.2005 Evaluate side-chains 152 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 148 time to evaluate : 0.776 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0629 time to fit residues: 1.4553 ------------------------------------------------------------------------------- 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: 59.7172 > 50: distance: 76 - 80: 15.248 distance: 80 - 81: 30.968 distance: 81 - 82: 28.111 distance: 81 - 84: 43.306 distance: 82 - 83: 22.487 distance: 82 - 88: 32.152 distance: 84 - 85: 40.386 distance: 84 - 86: 23.117 distance: 85 - 87: 13.862 distance: 88 - 89: 22.118 distance: 89 - 90: 19.546 distance: 89 - 92: 11.853 distance: 90 - 91: 16.866 distance: 90 - 100: 18.519 distance: 92 - 93: 8.268 distance: 93 - 94: 31.001 distance: 93 - 95: 6.078 distance: 94 - 96: 19.924 distance: 95 - 97: 22.824 distance: 96 - 98: 5.287 distance: 97 - 98: 21.348 distance: 98 - 99: 9.435 distance: 100 - 101: 17.695 distance: 101 - 102: 27.085 distance: 101 - 104: 10.442 distance: 102 - 103: 15.875 distance: 102 - 111: 20.332 distance: 104 - 105: 6.794 distance: 105 - 106: 10.035 distance: 106 - 107: 7.432 distance: 107 - 108: 10.607 distance: 108 - 109: 4.096 distance: 108 - 110: 4.783 distance: 111 - 112: 22.369 distance: 112 - 113: 59.717 distance: 112 - 115: 29.508 distance: 113 - 114: 16.535 distance: 113 - 116: 22.877 distance: 116 - 117: 27.683 distance: 117 - 118: 5.317 distance: 117 - 120: 37.631 distance: 118 - 119: 16.090 distance: 118 - 122: 3.458 distance: 120 - 121: 8.119 distance: 122 - 123: 23.982 distance: 123 - 124: 18.018 distance: 123 - 126: 17.730 distance: 124 - 125: 9.245 distance: 124 - 134: 16.407 distance: 126 - 127: 18.096 distance: 127 - 128: 16.031 distance: 127 - 129: 13.839 distance: 128 - 130: 14.736 distance: 129 - 131: 13.264 distance: 130 - 132: 4.764 distance: 131 - 132: 6.900 distance: 132 - 133: 15.264 distance: 134 - 135: 31.071 distance: 134 - 140: 33.508 distance: 135 - 136: 12.070 distance: 135 - 138: 48.574 distance: 136 - 137: 20.814 distance: 136 - 141: 33.533 distance: 138 - 139: 3.717 distance: 139 - 140: 16.541 distance: 141 - 142: 10.878 distance: 142 - 143: 25.597 distance: 142 - 145: 16.460 distance: 143 - 144: 50.077 distance: 143 - 152: 23.814 distance: 145 - 146: 25.703 distance: 146 - 147: 6.594 distance: 147 - 148: 26.527 distance: 148 - 149: 34.060 distance: 149 - 150: 35.262 distance: 149 - 151: 20.633 distance: 152 - 153: 19.453 distance: 153 - 154: 20.949 distance: 153 - 156: 26.973 distance: 154 - 155: 18.395 distance: 154 - 160: 24.983 distance: 156 - 157: 15.535 distance: 157 - 158: 13.766 distance: 157 - 159: 26.416 distance: 160 - 161: 20.132 distance: 160 - 166: 18.244 distance: 161 - 162: 12.355 distance: 161 - 164: 27.269 distance: 162 - 163: 45.684 distance: 162 - 167: 18.478 distance: 164 - 165: 10.827 distance: 165 - 166: 8.637