Starting phenix.real_space_refine on Sun Mar 10 15:35:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k45_22660/03_2024/7k45_22660.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k45_22660/03_2024/7k45_22660.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k45_22660/03_2024/7k45_22660.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k45_22660/03_2024/7k45_22660.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k45_22660/03_2024/7k45_22660.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k45_22660/03_2024/7k45_22660.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 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 16 5.16 5 C 1960 2.51 5 N 529 2.21 5 O 533 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 82": "OE1" <-> "OE2" Residue "L TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 80": "OE1" <-> "OE2" Residue "L PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 364": "OD1" <-> "OD2" Residue "B TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3038 Number of models: 1 Model: "" Number of chains: 4 Chain: "H" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 849 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 3, 'TRANS': 118} Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "L" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 730 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 96} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "B" Number of atoms: 1431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1431 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 11, 'TRANS': 182} Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 4, 'HIS:plan': 1, 'GLU:plan': 2, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 55 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.45, per 1000 atoms: 0.81 Number of scatterers: 3038 At special positions: 0 Unit cell: (70.35, 55.65, 100.8, 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 16 16.00 O 533 8.00 N 529 7.00 C 1960 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.02 Simple disulfide: pdb=" SG CYS H 101 " - pdb=" SG CYS H 106 " distance=2.05 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.10 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " 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 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " NAG-ASN " NAG A 1 " - " ASN B 343 " Time building additional restraints: 1.16 Conformation dependent library (CDL) restraints added in 517.5 milliseconds 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 764 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 10 sheets defined 15.3% alpha, 33.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'H' and resid 28 through 31 Processing helix chain 'H' and resid 64 through 66 No H-bonds generated for 'chain 'H' and resid 64 through 66' Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 30 through 32 No H-bonds generated for 'chain 'L' and resid 30 through 32' Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.745A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.815A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.227A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.295A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.052A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AA4, first strand: chain 'H' and resid 101 through 102 Processing sheet with id=AA5, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 11 removed outlier: 6.738A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 11 Processing sheet with id=AA8, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AA9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'B' and resid 473 through 474 126 hydrogen bonds defined for protein. 285 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: 0.92 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 933 1.33 - 1.47: 940 1.47 - 1.60: 1225 1.60 - 1.73: 2 1.73 - 1.86: 18 Bond restraints: 3118 Sorted by residual: bond pdb=" CB ILE L 2 " pdb=" CG1 ILE L 2 " ideal model delta sigma weight residual 1.530 1.611 -0.081 2.00e-02 2.50e+03 1.65e+01 bond pdb=" C5 NAG A 2 " pdb=" O5 NAG A 2 " ideal model delta sigma weight residual 1.413 1.479 -0.066 2.00e-02 2.50e+03 1.09e+01 bond pdb=" C5 NAG A 1 " pdb=" O5 NAG A 1 " ideal model delta sigma weight residual 1.413 1.474 -0.061 2.00e-02 2.50e+03 9.37e+00 bond pdb=" NE1 TRP H 50 " pdb=" CE2 TRP H 50 " ideal model delta sigma weight residual 1.370 1.337 0.033 1.10e-02 8.26e+03 8.78e+00 bond pdb=" CB ASN B 422 " pdb=" CG ASN B 422 " ideal model delta sigma weight residual 1.516 1.446 0.070 2.50e-02 1.60e+03 7.94e+00 ... (remaining 3113 not shown) Histogram of bond angle deviations from ideal: 97.98 - 105.20: 78 105.20 - 112.42: 1419 112.42 - 119.64: 1023 119.64 - 126.87: 1718 126.87 - 134.09: 29 Bond angle restraints: 4267 Sorted by residual: angle pdb=" C GLY H 8 " pdb=" N PRO H 9 " pdb=" CA PRO H 9 " ideal model delta sigma weight residual 120.03 128.19 -8.16 9.90e-01 1.02e+00 6.79e+01 angle pdb=" C ILE L 59 " pdb=" N PRO L 60 " pdb=" CA PRO L 60 " ideal model delta sigma weight residual 120.21 126.95 -6.74 9.60e-01 1.09e+00 4.93e+01 angle pdb=" C SER B 383 " pdb=" N PRO B 384 " pdb=" CA PRO B 384 " ideal model delta sigma weight residual 119.56 126.42 -6.86 1.02e+00 9.61e-01 4.53e+01 angle pdb=" C ALA B 520 " pdb=" N PRO B 521 " pdb=" CA PRO B 521 " ideal model delta sigma weight residual 119.56 126.33 -6.77 1.02e+00 9.61e-01 4.41e+01 angle pdb=" C GLN B 498 " pdb=" N PRO B 499 " pdb=" CA PRO B 499 " ideal model delta sigma weight residual 119.87 126.70 -6.83 1.04e+00 9.25e-01 4.31e+01 ... (remaining 4262 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.65: 1752 16.65 - 33.30: 55 33.30 - 49.94: 10 49.94 - 66.59: 4 66.59 - 83.24: 1 Dihedral angle restraints: 1822 sinusoidal: 618 harmonic: 1204 Sorted by residual: dihedral pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " pdb=" SG CYS B 525 " pdb=" CB CYS B 525 " ideal model delta sinusoidal sigma weight residual 93.00 121.87 -28.87 1 1.00e+01 1.00e-02 1.19e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 89 " pdb=" CB CYS L 89 " ideal model delta sinusoidal sigma weight residual 93.00 66.25 26.75 1 1.00e+01 1.00e-02 1.03e+01 dihedral pdb=" C TYR L 92 " pdb=" N TYR L 92 " pdb=" CA TYR L 92 " pdb=" CB TYR L 92 " ideal model delta harmonic sigma weight residual -122.60 -115.16 -7.44 0 2.50e+00 1.60e-01 8.85e+00 ... (remaining 1819 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 306 0.068 - 0.136: 127 0.136 - 0.204: 28 0.204 - 0.272: 5 0.272 - 0.340: 4 Chirality restraints: 470 Sorted by residual: chirality pdb=" C1 NAG A 2 " pdb=" O4 NAG A 1 " pdb=" C2 NAG A 2 " pdb=" O5 NAG A 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.54 0.14 2.00e-02 2.50e+03 4.64e+01 chirality pdb=" C2 NAG A 2 " pdb=" C1 NAG A 2 " pdb=" C3 NAG A 2 " pdb=" N2 NAG A 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.83 0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" C2 NAG A 1 " pdb=" C1 NAG A 1 " pdb=" C3 NAG A 1 " pdb=" N2 NAG A 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.82 0.33 2.00e-01 2.50e+01 2.65e+00 ... (remaining 467 not shown) Planarity restraints: 561 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR L 92 " -0.030 2.00e-02 2.50e+03 1.51e-02 4.56e+00 pdb=" CG TYR L 92 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR L 92 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR L 92 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR L 92 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR L 92 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR L 92 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR L 92 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 50 " 0.027 2.00e-02 2.50e+03 1.34e-02 4.49e+00 pdb=" CG TRP H 50 " -0.017 2.00e-02 2.50e+03 pdb=" CD1 TRP H 50 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP H 50 " -0.019 2.00e-02 2.50e+03 pdb=" NE1 TRP H 50 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP H 50 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP H 50 " -0.012 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 50 " 0.008 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 50 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP H 50 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 47 " -0.023 2.00e-02 2.50e+03 1.32e-02 4.34e+00 pdb=" CG TRP H 47 " 0.013 2.00e-02 2.50e+03 pdb=" CD1 TRP H 47 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP H 47 " 0.018 2.00e-02 2.50e+03 pdb=" NE1 TRP H 47 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP H 47 " 0.011 2.00e-02 2.50e+03 pdb=" CE3 TRP H 47 " 0.014 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 47 " -0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 47 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP H 47 " -0.017 2.00e-02 2.50e+03 ... (remaining 558 not shown) Histogram of nonbonded interaction distances: 2.57 - 3.03: 1766 3.03 - 3.50: 2712 3.50 - 3.97: 4880 3.97 - 4.43: 5575 4.43 - 4.90: 9162 Nonbonded interactions: 24095 Sorted by model distance: nonbonded pdb=" N LYS B 462 " pdb=" O LYS B 462 " model vdw 2.568 2.496 nonbonded pdb=" N GLU L 80 " pdb=" O GLU L 80 " model vdw 2.592 2.496 nonbonded pdb=" CB GLN H 6 " pdb=" OE1 GLN H 6 " model vdw 2.598 2.752 nonbonded pdb=" N GLY B 502 " pdb=" O GLY B 502 " model vdw 2.601 2.496 nonbonded pdb=" N SER B 373 " pdb=" N PHE B 374 " model vdw 2.605 2.560 ... (remaining 24090 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 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 25.640 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.070 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 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 : 0.014 0.092 3118 Z= 0.969 Angle : 1.416 8.157 4267 Z= 0.963 Chirality : 0.079 0.340 470 Planarity : 0.006 0.039 560 Dihedral : 9.350 83.236 1037 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 0.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.92 (0.41), residues: 411 helix: -4.00 (0.49), residues: 33 sheet: 1.14 (0.43), residues: 150 loop : 1.17 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.008 TRP H 50 HIS 0.002 0.001 HIS H 65 PHE 0.013 0.003 PHE H 64 TYR 0.030 0.004 TYR L 92 ARG 0.004 0.000 ARG H 67 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: B 369 TYR cc_start: 0.7080 (t80) cc_final: 0.6653 (t80) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.2230 time to fit residues: 21.3515 Evaluate side-chains 44 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.0980 chunk 31 optimal weight: 0.5980 chunk 17 optimal weight: 0.0980 chunk 10 optimal weight: 0.4980 chunk 20 optimal weight: 0.4980 chunk 16 optimal weight: 0.0980 chunk 32 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 19 optimal weight: 0.3980 chunk 23 optimal weight: 0.0770 chunk 37 optimal weight: 0.0980 overall best weight: 0.0938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 35 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 3118 Z= 0.187 Angle : 0.630 5.939 4267 Z= 0.336 Chirality : 0.047 0.139 470 Planarity : 0.004 0.036 560 Dihedral : 4.842 21.669 502 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 3.24 % Allowed : 12.55 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.71 (0.41), residues: 411 helix: -3.60 (0.67), residues: 27 sheet: 0.77 (0.41), residues: 150 loop : 0.97 (0.40), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.002 0.002 HIS H 65 PHE 0.014 0.002 PHE B 497 TYR 0.020 0.002 TYR L 92 ARG 0.004 0.001 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 56 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 37 TYR cc_start: 0.8581 (m-10) cc_final: 0.8031 (m-80) REVERT: L 72 PHE cc_start: 0.6717 (m-80) cc_final: 0.6504 (m-80) outliers start: 8 outliers final: 6 residues processed: 63 average time/residue: 0.1748 time to fit residues: 13.0996 Evaluate side-chains 53 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 47 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 35 GLN Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 480 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 12 optimal weight: 0.1980 chunk 29 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 6 GLN ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 3118 Z= 0.458 Angle : 0.723 6.888 4267 Z= 0.389 Chirality : 0.049 0.137 470 Planarity : 0.005 0.038 560 Dihedral : 5.423 25.502 502 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 4.05 % Allowed : 14.98 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.40), residues: 411 helix: -3.37 (0.97), residues: 20 sheet: 0.32 (0.40), residues: 152 loop : 0.54 (0.39), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP L 36 HIS 0.007 0.004 HIS H 65 PHE 0.014 0.002 PHE B 347 TYR 0.031 0.003 TYR L 92 ARG 0.005 0.001 ARG L 62 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 47 time to evaluate : 0.352 Fit side-chains revert: symmetry clash REVERT: H 90 ASP cc_start: 0.7978 (m-30) cc_final: 0.7752 (m-30) REVERT: L 72 PHE cc_start: 0.7196 (m-80) cc_final: 0.6791 (m-10) REVERT: B 369 TYR cc_start: 0.7316 (t80) cc_final: 0.6854 (t80) outliers start: 10 outliers final: 8 residues processed: 54 average time/residue: 0.1877 time to fit residues: 12.1555 Evaluate side-chains 48 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 40 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 480 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 1.9990 chunk 28 optimal weight: 0.3980 chunk 19 optimal weight: 0.0970 chunk 4 optimal weight: 0.0770 chunk 17 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 39 optimal weight: 0.3980 chunk 35 optimal weight: 0.3980 chunk 10 optimal weight: 0.9990 chunk 33 optimal weight: 0.0070 overall best weight: 0.1954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 35 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.3767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3118 Z= 0.218 Angle : 0.620 6.965 4267 Z= 0.333 Chirality : 0.047 0.140 470 Planarity : 0.004 0.036 560 Dihedral : 5.099 24.772 502 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 4.05 % Allowed : 14.98 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.40), residues: 411 helix: -3.54 (0.80), residues: 27 sheet: 0.21 (0.40), residues: 152 loop : 0.75 (0.40), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.002 0.001 HIS H 65 PHE 0.019 0.001 PHE B 392 TYR 0.024 0.001 TYR L 92 ARG 0.008 0.001 ARG L 55 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 45 time to evaluate : 0.524 Fit side-chains revert: symmetry clash REVERT: L 72 PHE cc_start: 0.7176 (m-80) cc_final: 0.6724 (m-10) REVERT: L 74 LEU cc_start: 0.8643 (tt) cc_final: 0.8409 (tt) REVERT: B 369 TYR cc_start: 0.7303 (t80) cc_final: 0.6744 (t80) outliers start: 10 outliers final: 7 residues processed: 53 average time/residue: 0.1927 time to fit residues: 12.0644 Evaluate side-chains 50 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 43 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 35 GLN Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 480 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 0.4980 chunk 0 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 27 optimal weight: 0.2980 chunk 20 optimal weight: 0.2980 chunk 35 optimal weight: 0.0970 chunk 10 optimal weight: 0.9980 chunk 13 optimal weight: 0.0000 chunk 7 optimal weight: 0.9990 overall best weight: 0.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 35 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.3982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3118 Z= 0.227 Angle : 0.591 6.211 4267 Z= 0.316 Chirality : 0.047 0.137 470 Planarity : 0.004 0.040 560 Dihedral : 4.857 24.860 502 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.05 % Allowed : 15.79 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.26 (0.41), residues: 411 helix: -2.81 (1.11), residues: 20 sheet: 0.25 (0.40), residues: 149 loop : 0.56 (0.40), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 36 HIS 0.003 0.002 HIS H 65 PHE 0.015 0.001 PHE B 392 TYR 0.024 0.001 TYR L 92 ARG 0.009 0.001 ARG L 55 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 47 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: H 90 ASP cc_start: 0.7828 (m-30) cc_final: 0.7201 (m-30) REVERT: L 37 TYR cc_start: 0.8724 (m-10) cc_final: 0.7782 (m-80) REVERT: L 74 LEU cc_start: 0.8627 (tt) cc_final: 0.8411 (tt) REVERT: B 369 TYR cc_start: 0.7316 (t80) cc_final: 0.6697 (t80) REVERT: B 408 ARG cc_start: 0.7471 (ttp80) cc_final: 0.7257 (ttp80) outliers start: 10 outliers final: 7 residues processed: 55 average time/residue: 0.2184 time to fit residues: 14.0744 Evaluate side-chains 49 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 42 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 480 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 0.1980 chunk 9 optimal weight: 0.9980 chunk 39 optimal weight: 0.3980 chunk 32 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 4 optimal weight: 0.0770 chunk 22 optimal weight: 0.0070 overall best weight: 0.2756 ------------------------------------------------------------------------------- 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: 0.4323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3118 Z= 0.245 Angle : 0.597 6.221 4267 Z= 0.318 Chirality : 0.046 0.155 470 Planarity : 0.004 0.045 560 Dihedral : 4.792 26.413 502 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 5.26 % Allowed : 14.57 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.17 (0.41), residues: 411 helix: -2.77 (1.10), residues: 20 sheet: 0.18 (0.40), residues: 151 loop : 0.49 (0.41), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 436 HIS 0.003 0.002 HIS H 65 PHE 0.012 0.001 PHE B 392 TYR 0.024 0.002 TYR L 92 ARG 0.007 0.001 ARG L 55 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 45 time to evaluate : 0.326 Fit side-chains revert: symmetry clash REVERT: B 369 TYR cc_start: 0.7262 (t80) cc_final: 0.6573 (t80) REVERT: B 430 THR cc_start: 0.8397 (m) cc_final: 0.8162 (p) outliers start: 13 outliers final: 10 residues processed: 53 average time/residue: 0.2112 time to fit residues: 12.9764 Evaluate side-chains 50 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 40 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 35 GLN Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 471 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.8980 chunk 22 optimal weight: 0.1980 chunk 33 optimal weight: 0.9990 chunk 39 optimal weight: 0.3980 chunk 24 optimal weight: 0.0970 chunk 18 optimal weight: 0.9990 chunk 15 optimal weight: 0.4980 chunk 23 optimal weight: 0.4980 chunk 11 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 25 optimal weight: 0.1980 overall best weight: 0.2778 ------------------------------------------------------------------------------- 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: 0.7820 moved from start: 0.4498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3118 Z= 0.241 Angle : 0.587 4.922 4267 Z= 0.313 Chirality : 0.046 0.139 470 Planarity : 0.005 0.049 560 Dihedral : 4.768 28.208 502 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 4.86 % Allowed : 14.57 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.09 (0.41), residues: 411 helix: -2.91 (1.04), residues: 20 sheet: 0.17 (0.40), residues: 151 loop : 0.41 (0.42), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 436 HIS 0.003 0.002 HIS H 65 PHE 0.009 0.001 PHE B 392 TYR 0.022 0.001 TYR L 92 ARG 0.011 0.001 ARG L 55 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 44 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: H 90 ASP cc_start: 0.7901 (m-30) cc_final: 0.7351 (m-30) REVERT: B 430 THR cc_start: 0.8182 (m) cc_final: 0.7963 (p) outliers start: 12 outliers final: 10 residues processed: 52 average time/residue: 0.2186 time to fit residues: 13.2170 Evaluate side-chains 53 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 43 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 35 GLN Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 471 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-dev-5265/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-dev-5265/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-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-dev-5265/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-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-dev-5265/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-dev-5265/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-dev-5265/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-dev-5265/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: 70.9734 > 50: distance: 23 - 161: 34.526 distance: 24 - 155: 36.747 distance: 27 - 152: 34.089 distance: 83 - 88: 35.839 distance: 89 - 90: 39.362 distance: 90 - 91: 39.014 distance: 92 - 93: 40.290 distance: 93 - 94: 39.306 distance: 93 - 95: 55.654 distance: 94 - 96: 39.977 distance: 95 - 97: 40.063 distance: 96 - 98: 40.651 distance: 97 - 98: 57.537 distance: 98 - 99: 55.676 distance: 100 - 101: 43.957 distance: 101 - 102: 45.916 distance: 101 - 104: 24.165 distance: 102 - 103: 39.057 distance: 104 - 105: 12.892 distance: 105 - 106: 41.102 distance: 106 - 107: 24.978 distance: 107 - 108: 58.498 distance: 109 - 110: 25.818 distance: 110 - 111: 19.112 distance: 110 - 113: 49.280 distance: 111 - 112: 28.354 distance: 111 - 117: 47.701 distance: 113 - 114: 46.063 distance: 114 - 115: 55.764 distance: 114 - 116: 55.126 distance: 117 - 118: 39.439 distance: 119 - 124: 18.462 distance: 121 - 122: 40.452 distance: 124 - 125: 60.255 distance: 125 - 128: 30.079 distance: 126 - 127: 16.555 distance: 126 - 129: 18.608 distance: 129 - 130: 23.140 distance: 130 - 131: 50.493 distance: 130 - 133: 11.155 distance: 131 - 132: 56.697 distance: 131 - 134: 55.571 distance: 134 - 135: 55.896 distance: 135 - 138: 47.331 distance: 136 - 145: 39.845 distance: 138 - 139: 49.560 distance: 139 - 140: 41.969 distance: 139 - 141: 23.313 distance: 140 - 142: 47.172 distance: 142 - 144: 23.872 distance: 143 - 144: 16.953 distance: 146 - 147: 40.086 distance: 146 - 149: 56.649 distance: 147 - 148: 39.509 distance: 149 - 150: 57.565 distance: 149 - 151: 57.969 distance: 153 - 154: 39.151 distance: 154 - 155: 68.570 distance: 154 - 156: 40.498 distance: 156 - 203: 32.845 distance: 157 - 158: 41.330 distance: 157 - 160: 55.823 distance: 158 - 159: 54.868 distance: 158 - 162: 32.723 distance: 159 - 200: 37.978