Starting phenix.real_space_refine on Fri Jul 19 02:48:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pq2_17819/07_2024/8pq2_17819_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pq2_17819/07_2024/8pq2_17819.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pq2_17819/07_2024/8pq2_17819.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pq2_17819/07_2024/8pq2_17819.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pq2_17819/07_2024/8pq2_17819_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pq2_17819/07_2024/8pq2_17819_trim.cif" } resolution = 3.85 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 15 5.16 5 C 1962 2.51 5 N 511 2.21 5 O 577 1.98 5 H 2891 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 5956 Number of models: 1 Model: "" Number of chains: 4 Chain: "H" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 1752 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 1273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1273 Classifications: {'peptide': 85} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 78} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 2917 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 12, 'TRANS': 177} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.92, per 1000 atoms: 0.66 Number of scatterers: 5956 At special positions: 0 Unit cell: (65.9412, 79.8903, 103.984, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 15 16.00 O 577 8.00 N 511 7.00 C 1962 6.00 H 2891 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 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 NAG-ASN " NAG C 601 " - " ASN C 343 " Time building additional restraints: 4.24 Conformation dependent library (CDL) restraints added in 629.9 milliseconds 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 720 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 8 sheets defined 6.7% alpha, 34.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.913A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 3.562A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE C 371 " --> pdb=" O ILE C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.668A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.474A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 5 through 8 Processing sheet with id=AA2, first strand: chain 'H' and resid 58 through 59 removed outlier: 6.250A pdb=" N LEU H 45 " --> pdb=" O SER H 40 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N SER H 40 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N CYS H 95 " --> pdb=" O TRP H 111 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N TRP H 111 " --> pdb=" O CYS H 95 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ARG H 97 " --> pdb=" O ASP H 109 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N SER H 99 " --> pdb=" O ARG H 107 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ARG H 107 " --> pdb=" O SER H 99 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 58 through 59 removed outlier: 6.250A pdb=" N LEU H 45 " --> pdb=" O SER H 40 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N SER H 40 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 19 through 24 removed outlier: 4.192A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE L 75 " --> pdb=" O VAL L 19 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 34 through 39 removed outlier: 6.635A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N LYS L 39 " --> pdb=" O ALA L 43 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N ALA L 43 " --> pdb=" O LYS L 39 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AA7, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'C' and resid 473 through 474 94 hydrogen bonds defined for protein. 222 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: 1.92 Time building geometry restraints manager: 4.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 2881 1.04 - 1.23: 89 1.23 - 1.43: 1332 1.43 - 1.63: 1726 1.63 - 1.82: 18 Bond restraints: 6046 Sorted by residual: bond pdb=" C1 NAG C 601 " pdb=" O5 NAG C 601 " ideal model delta sigma weight residual 1.406 1.430 -0.024 2.00e-02 2.50e+03 1.50e+00 bond pdb=" C5 NAG C 601 " pdb=" O5 NAG C 601 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.22e+00 bond pdb=" C3 NAG C 601 " pdb=" O3 NAG C 601 " ideal model delta sigma weight residual 1.403 1.423 -0.020 2.00e-02 2.50e+03 9.94e-01 bond pdb=" C2 NAG C 601 " pdb=" N2 NAG C 601 " ideal model delta sigma weight residual 1.439 1.454 -0.015 2.00e-02 2.50e+03 5.45e-01 bond pdb=" C4 NAG C 601 " pdb=" O4 NAG C 601 " ideal model delta sigma weight residual 1.409 1.423 -0.014 2.00e-02 2.50e+03 4.81e-01 ... (remaining 6041 not shown) Histogram of bond angle deviations from ideal: 100.81 - 107.44: 213 107.44 - 114.07: 6869 114.07 - 120.70: 2024 120.70 - 127.33: 1672 127.33 - 133.96: 45 Bond angle restraints: 10823 Sorted by residual: angle pdb=" N THR L 69 " pdb=" CA THR L 69 " pdb=" CB THR L 69 " ideal model delta sigma weight residual 113.89 109.86 4.03 1.93e+00 2.68e-01 4.35e+00 angle pdb=" C GLY L 68 " pdb=" N THR L 69 " pdb=" CA THR L 69 " ideal model delta sigma weight residual 124.82 121.83 2.99 1.78e+00 3.16e-01 2.83e+00 angle pdb=" C SER L 60 " pdb=" CA SER L 60 " pdb=" CB SER L 60 " ideal model delta sigma weight residual 111.50 109.34 2.16 1.29e+00 6.01e-01 2.79e+00 angle pdb=" C PHE H 33 " pdb=" N TRP H 34 " pdb=" CA TRP H 34 " ideal model delta sigma weight residual 122.77 120.73 2.04 1.41e+00 5.03e-01 2.10e+00 angle pdb=" C ALA L 43 " pdb=" CA ALA L 43 " pdb=" CB ALA L 43 " ideal model delta sigma weight residual 109.46 111.70 -2.24 1.64e+00 3.72e-01 1.87e+00 ... (remaining 10818 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.34: 2773 17.34 - 34.68: 109 34.68 - 52.02: 54 52.02 - 69.36: 19 69.36 - 86.69: 3 Dihedral angle restraints: 2958 sinusoidal: 1542 harmonic: 1416 Sorted by residual: dihedral pdb=" CA PRO L 59 " pdb=" C PRO L 59 " pdb=" N SER L 60 " pdb=" CA SER L 60 " ideal model delta harmonic sigma weight residual -180.00 -162.97 -17.03 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" N LYS L 39 " pdb=" CA LYS L 39 " pdb=" CB LYS L 39 " pdb=" CG LYS L 39 " ideal model delta sinusoidal sigma weight residual -60.00 -117.36 57.36 3 1.50e+01 4.44e-03 9.44e+00 dihedral pdb=" CB LYS L 39 " pdb=" CG LYS L 39 " pdb=" CD LYS L 39 " pdb=" CE LYS L 39 " ideal model delta sinusoidal sigma weight residual -180.00 -123.99 -56.01 3 1.50e+01 4.44e-03 9.38e+00 ... (remaining 2955 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 259 0.029 - 0.058: 147 0.058 - 0.087: 21 0.087 - 0.116: 30 0.116 - 0.145: 7 Chirality restraints: 464 Sorted by residual: chirality pdb=" C1 NAG C 601 " pdb=" ND2 ASN C 343 " pdb=" C2 NAG C 601 " pdb=" O5 NAG C 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 5.23e-01 chirality pdb=" CA ILE C 434 " pdb=" N ILE C 434 " pdb=" C ILE C 434 " pdb=" CB ILE C 434 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.37e-01 chirality pdb=" CA VAL C 362 " pdb=" N VAL C 362 " pdb=" C VAL C 362 " pdb=" CB VAL C 362 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.01e-01 ... (remaining 461 not shown) Planarity restraints: 916 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS C 336 " -0.019 5.00e-02 4.00e+02 2.84e-02 1.29e+00 pdb=" N PRO C 337 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO C 337 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO C 337 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL L 58 " -0.016 5.00e-02 4.00e+02 2.38e-02 9.07e-01 pdb=" N PRO L 59 " 0.041 5.00e-02 4.00e+02 pdb=" CA PRO L 59 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO L 59 " -0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR L 36 " 0.005 2.00e-02 2.50e+03 9.23e-03 8.52e-01 pdb=" C TYR L 36 " -0.016 2.00e-02 2.50e+03 pdb=" O TYR L 36 " 0.006 2.00e-02 2.50e+03 pdb=" N GLN L 37 " 0.005 2.00e-02 2.50e+03 ... (remaining 913 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 345 2.20 - 2.80: 11960 2.80 - 3.40: 14397 3.40 - 4.00: 19307 4.00 - 4.60: 28938 Nonbonded interactions: 74947 Sorted by model distance: nonbonded pdb=" HE2 HIS C 339 " pdb=" O7 NAG C 601 " model vdw 1.602 1.850 nonbonded pdb=" OD1 ASP H 98 " pdb=" H GLY H 108 " model vdw 1.623 1.850 nonbonded pdb=" OE1 GLN C 493 " pdb=" H SER C 494 " model vdw 1.668 1.850 nonbonded pdb="HH22 ARG H 66 " pdb=" OD2 ASP H 89 " model vdw 1.670 1.850 nonbonded pdb="HH12 ARG C 457 " pdb=" OD2 ASP C 467 " model vdw 1.690 1.850 ... (remaining 74942 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: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.750 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: 0.080 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 23.150 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 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 : 0.002 0.024 3155 Z= 0.151 Angle : 0.510 4.411 4301 Z= 0.265 Chirality : 0.043 0.145 464 Planarity : 0.003 0.028 551 Dihedral : 10.370 74.805 1115 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 2.73 % Allowed : 3.33 % Favored : 93.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -2.04 (0.40), residues: 384 helix: -2.37 (1.01), residues: 29 sheet: -0.21 (0.45), residues: 116 loop : -1.91 (0.38), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 7 HIS 0.001 0.000 HIS C 339 PHE 0.007 0.001 PHE H 33 TYR 0.008 0.001 TYR H 94 ARG 0.001 0.000 ARG C 457 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 424 is missing expected H atoms. Skipping. Evaluate side-chains 82 residues out of total 335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 73 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 74 THR cc_start: 0.8186 (m) cc_final: 0.7806 (p) REVERT: L 85 THR cc_start: 0.8472 (m) cc_final: 0.7972 (p) REVERT: C 353 TRP cc_start: 0.9135 (p-90) cc_final: 0.8920 (p-90) REVERT: C 474 GLN cc_start: 0.7895 (tt0) cc_final: 0.7378 (tt0) outliers start: 9 outliers final: 4 residues processed: 79 average time/residue: 0.3370 time to fit residues: 31.5387 Evaluate side-chains 55 residues out of total 335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 51 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 81 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 0.0170 chunk 18 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 487 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3155 Z= 0.197 Angle : 0.543 5.388 4301 Z= 0.275 Chirality : 0.044 0.151 464 Planarity : 0.003 0.029 551 Dihedral : 6.796 73.751 458 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 1.82 % Allowed : 10.91 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -2.12 (0.40), residues: 384 helix: -2.99 (0.94), residues: 29 sheet: -0.47 (0.44), residues: 123 loop : -1.78 (0.38), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 35 HIS 0.001 0.000 HIS L 50 PHE 0.027 0.001 PHE H 29 TYR 0.010 0.001 TYR H 94 ARG 0.001 0.000 ARG C 466 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 424 is missing expected H atoms. Skipping. Evaluate side-chains 60 residues out of total 335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 54 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 74 THR cc_start: 0.8181 (m) cc_final: 0.7826 (p) REVERT: C 378 LYS cc_start: 0.7690 (ttmm) cc_final: 0.7149 (ttmm) outliers start: 6 outliers final: 6 residues processed: 58 average time/residue: 0.3008 time to fit residues: 21.2322 Evaluate side-chains 58 residues out of total 335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 52 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 94 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 28 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 37 optimal weight: 0.0270 chunk 30 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 50 HIS ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3155 Z= 0.176 Angle : 0.526 5.407 4301 Z= 0.266 Chirality : 0.043 0.145 464 Planarity : 0.003 0.029 551 Dihedral : 6.709 76.005 458 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 3.64 % Allowed : 11.21 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -2.07 (0.40), residues: 384 helix: -2.79 (0.97), residues: 29 sheet: -0.34 (0.45), residues: 119 loop : -1.81 (0.37), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 35 HIS 0.001 0.000 HIS C 339 PHE 0.017 0.001 PHE H 29 TYR 0.010 0.001 TYR H 94 ARG 0.001 0.000 ARG C 466 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 424 is missing expected H atoms. Skipping. Evaluate side-chains 64 residues out of total 335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 52 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 74 THR cc_start: 0.8197 (m) cc_final: 0.7840 (p) outliers start: 12 outliers final: 9 residues processed: 60 average time/residue: 0.2987 time to fit residues: 21.8286 Evaluate side-chains 58 residues out of total 335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 49 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain C residue 361 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 16 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 36 optimal weight: 0.1980 chunk 18 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 50 HIS ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3155 Z= 0.204 Angle : 0.535 5.633 4301 Z= 0.273 Chirality : 0.043 0.149 464 Planarity : 0.004 0.029 551 Dihedral : 6.712 76.789 458 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.38 % Favored : 90.62 % Rotamer: Outliers : 3.94 % Allowed : 11.21 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -2.12 (0.40), residues: 384 helix: -2.71 (0.98), residues: 29 sheet: -0.40 (0.46), residues: 119 loop : -1.85 (0.37), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 35 HIS 0.001 0.000 HIS H 53 PHE 0.039 0.002 PHE H 29 TYR 0.011 0.001 TYR H 94 ARG 0.002 0.000 ARG C 466 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 424 is missing expected H atoms. Skipping. Evaluate side-chains 63 residues out of total 335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 50 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 74 THR cc_start: 0.8210 (m) cc_final: 0.7846 (p) REVERT: C 378 LYS cc_start: 0.7686 (ttmm) cc_final: 0.7113 (ttmm) outliers start: 13 outliers final: 13 residues processed: 57 average time/residue: 0.3426 time to fit residues: 24.0664 Evaluate side-chains 63 residues out of total 335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 50 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 50 HIS Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 430 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 15 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 50 HIS ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3155 Z= 0.236 Angle : 0.546 5.493 4301 Z= 0.281 Chirality : 0.044 0.155 464 Planarity : 0.004 0.029 551 Dihedral : 6.738 77.288 458 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.68 % Favored : 89.32 % Rotamer: Outliers : 3.64 % Allowed : 11.82 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -2.20 (0.40), residues: 384 helix: -2.23 (1.14), residues: 24 sheet: -0.43 (0.45), residues: 119 loop : -2.02 (0.37), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 35 HIS 0.002 0.001 HIS L 53 PHE 0.030 0.002 PHE H 29 TYR 0.016 0.001 TYR L 49 ARG 0.002 0.000 ARG C 466 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 424 is missing expected H atoms. Skipping. Evaluate side-chains 62 residues out of total 335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 50 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 74 THR cc_start: 0.8211 (m) cc_final: 0.7839 (p) REVERT: C 378 LYS cc_start: 0.7677 (ttmm) cc_final: 0.7101 (ttmm) outliers start: 12 outliers final: 10 residues processed: 56 average time/residue: 0.3157 time to fit residues: 21.6438 Evaluate side-chains 59 residues out of total 335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 49 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 430 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 9 optimal weight: 0.9990 chunk 36 optimal weight: 0.0980 chunk 30 optimal weight: 0.6980 chunk 17 optimal weight: 0.2980 chunk 3 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 20 optimal weight: 0.3980 chunk 26 optimal weight: 0.7980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 50 HIS ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3155 Z= 0.151 Angle : 0.508 5.342 4301 Z= 0.257 Chirality : 0.043 0.150 464 Planarity : 0.003 0.032 551 Dihedral : 6.193 77.013 454 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 3.64 % Allowed : 11.82 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -2.18 (0.40), residues: 384 helix: -2.76 (0.96), residues: 30 sheet: -0.56 (0.45), residues: 123 loop : -1.82 (0.38), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 7 HIS 0.001 0.000 HIS L 50 PHE 0.024 0.001 PHE H 29 TYR 0.009 0.001 TYR H 94 ARG 0.001 0.000 ARG C 466 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 424 is missing expected H atoms. Skipping. Evaluate side-chains 63 residues out of total 335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 51 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 61 ARG cc_start: 0.7197 (tpp-160) cc_final: 0.6797 (tpp-160) REVERT: L 74 THR cc_start: 0.8203 (m) cc_final: 0.7840 (p) REVERT: C 378 LYS cc_start: 0.7622 (ttmm) cc_final: 0.7049 (ttmm) outliers start: 12 outliers final: 10 residues processed: 59 average time/residue: 0.2955 time to fit residues: 21.4258 Evaluate side-chains 58 residues out of total 335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 48 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 50 HIS Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 94 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 20 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 50 HIS ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3155 Z= 0.242 Angle : 0.550 5.186 4301 Z= 0.283 Chirality : 0.044 0.157 464 Planarity : 0.004 0.031 551 Dihedral : 6.474 76.888 454 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.50 % Favored : 87.50 % Rotamer: Outliers : 3.33 % Allowed : 12.73 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -2.29 (0.40), residues: 384 helix: -2.30 (1.11), residues: 24 sheet: -0.64 (0.44), residues: 123 loop : -2.01 (0.37), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 47 HIS 0.010 0.001 HIS L 50 PHE 0.023 0.001 PHE H 29 TYR 0.018 0.001 TYR L 49 ARG 0.002 0.000 ARG C 466 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 424 is missing expected H atoms. Skipping. Evaluate side-chains 58 residues out of total 335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 47 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 74 THR cc_start: 0.8226 (m) cc_final: 0.7836 (p) REVERT: C 378 LYS cc_start: 0.7660 (ttmm) cc_final: 0.7070 (ttmm) outliers start: 11 outliers final: 10 residues processed: 53 average time/residue: 0.3161 time to fit residues: 20.2702 Evaluate side-chains 57 residues out of total 335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 47 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 430 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 18 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 33 optimal weight: 0.2980 chunk 35 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 50 HIS ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3155 Z= 0.178 Angle : 0.521 5.116 4301 Z= 0.265 Chirality : 0.043 0.155 464 Planarity : 0.004 0.031 551 Dihedral : 6.352 77.389 454 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 3.33 % Allowed : 13.03 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -2.25 (0.40), residues: 384 helix: -2.22 (1.13), residues: 24 sheet: -0.50 (0.45), residues: 119 loop : -2.04 (0.36), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 35 HIS 0.002 0.000 HIS L 50 PHE 0.021 0.001 PHE H 29 TYR 0.010 0.001 TYR H 94 ARG 0.001 0.000 ARG C 466 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 424 is missing expected H atoms. Skipping. Evaluate side-chains 59 residues out of total 335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 48 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 74 THR cc_start: 0.8189 (m) cc_final: 0.7820 (p) REVERT: C 378 LYS cc_start: 0.7630 (ttmm) cc_final: 0.7050 (ttmm) outliers start: 11 outliers final: 10 residues processed: 54 average time/residue: 0.3163 time to fit residues: 20.7434 Evaluate side-chains 57 residues out of total 335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 47 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 430 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 30 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN L 50 HIS ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3155 Z= 0.232 Angle : 0.543 5.229 4301 Z= 0.280 Chirality : 0.044 0.163 464 Planarity : 0.004 0.032 551 Dihedral : 6.400 77.355 454 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.24 % Favored : 87.76 % Rotamer: Outliers : 3.64 % Allowed : 12.73 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -2.37 (0.39), residues: 384 helix: -2.35 (1.11), residues: 24 sheet: -0.56 (0.45), residues: 119 loop : -2.12 (0.36), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 47 HIS 0.001 0.000 HIS L 50 PHE 0.039 0.002 PHE H 29 TYR 0.013 0.001 TYR H 94 ARG 0.002 0.000 ARG C 498 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 424 is missing expected H atoms. Skipping. Evaluate side-chains 58 residues out of total 335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 46 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 74 THR cc_start: 0.8235 (m) cc_final: 0.7841 (p) outliers start: 12 outliers final: 10 residues processed: 53 average time/residue: 0.3548 time to fit residues: 22.7342 Evaluate side-chains 55 residues out of total 335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 45 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 430 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 23 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 58 ASN L 50 HIS ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3155 Z= 0.213 Angle : 0.551 6.199 4301 Z= 0.282 Chirality : 0.044 0.163 464 Planarity : 0.004 0.031 551 Dihedral : 6.388 77.619 454 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.90 % Favored : 90.10 % Rotamer: Outliers : 3.64 % Allowed : 11.82 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -2.27 (0.40), residues: 384 helix: -2.17 (1.15), residues: 23 sheet: -0.37 (0.46), residues: 115 loop : -2.12 (0.36), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 47 HIS 0.001 0.000 HIS L 50 PHE 0.039 0.002 PHE H 29 TYR 0.012 0.001 TYR H 94 ARG 0.001 0.000 ARG C 466 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 424 is missing expected H atoms. Skipping. Evaluate side-chains 58 residues out of total 335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 46 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 74 THR cc_start: 0.8202 (m) cc_final: 0.7826 (p) outliers start: 12 outliers final: 11 residues processed: 53 average time/residue: 0.3584 time to fit residues: 22.7012 Evaluate side-chains 57 residues out of total 335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 46 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 430 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 26 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 37 optimal weight: 0.4980 chunk 0 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 50 HIS ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.108766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.091191 restraints weight = 17066.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.095408 restraints weight = 8352.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.098359 restraints weight = 5166.273| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3155 Z= 0.191 Angle : 0.537 5.802 4301 Z= 0.274 Chirality : 0.044 0.164 464 Planarity : 0.004 0.030 551 Dihedral : 6.323 77.431 454 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.20 % Favored : 88.80 % Rotamer: Outliers : 3.64 % Allowed : 11.82 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -2.27 (0.40), residues: 384 helix: -2.13 (1.16), residues: 23 sheet: -0.38 (0.46), residues: 115 loop : -2.13 (0.36), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 47 HIS 0.001 0.000 HIS L 50 PHE 0.038 0.001 PHE H 29 TYR 0.011 0.001 TYR H 94 ARG 0.001 0.000 ARG C 466 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2631.66 seconds wall clock time: 46 minutes 7.58 seconds (2767.58 seconds total)