Starting phenix.real_space_refine on Sun Mar 10 20:35:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x26_32959/03_2024/7x26_32959_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x26_32959/03_2024/7x26_32959.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.685 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x26_32959/03_2024/7x26_32959.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x26_32959/03_2024/7x26_32959.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x26_32959/03_2024/7x26_32959_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x26_32959/03_2024/7x26_32959_neut.pdb" } resolution = 3.685 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= 0.001 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 21 5.16 5 C 3040 2.51 5 N 803 2.21 5 O 964 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H ARG 50": "NH1" <-> "NH2" Residue "H ARG 59": "NH1" <-> "NH2" Residue "H TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 98": "NH1" <-> "NH2" Residue "H ARG 217": "NH1" <-> "NH2" Residue "I GLU 382": "OE1" <-> "OE2" Residue "I ARG 505": "NH1" <-> "NH2" Residue "K ARG 40": "NH1" <-> "NH2" Residue "K TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 109": "NH1" <-> "NH2" Residue "K GLU 144": "OE1" <-> "OE2" Residue "K GLU 196": "OE1" <-> "OE2" 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: 4828 Number of models: 1 Model: "" Number of chains: 3 Chain: "H" Number of atoms: 1633 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 221, 1627 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 208} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 221, 1627 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 208} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 bond proxies already assigned to first conformer: 1655 Chain: "I" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1594 Classifications: {'peptide': 208} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 2, 'PTRANS': 14, 'TRANS': 191} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "K" Number of atoms: 1601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1601 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 199} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'ASP:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 24 Time building chain proxies: 3.84, per 1000 atoms: 0.80 Number of scatterers: 4828 At special positions: 0 Unit cell: (79.0225, 83.3525, 130.982, 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 21 16.00 O 964 8.00 N 803 7.00 C 3040 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 147 " - pdb=" SG CYS H 203 " distance=2.01 Simple disulfide: pdb=" SG CYS I 383 " - pdb=" SG CYS I 407 " distance=2.02 Simple disulfide: pdb=" SG CYS I 425 " - pdb=" SG CYS I 478 " distance=2.03 Simple disulfide: pdb=" SG CYS I 437 " - pdb=" SG CYS I 585 " distance=2.06 Simple disulfide: pdb=" SG CYS I 503 " - pdb=" SG CYS I 526 " distance=2.02 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 89 " distance=2.04 Simple disulfide: pdb=" SG CYS K 135 " - pdb=" SG CYS K 195 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.61 Conformation dependent library (CDL) restraints added in 1.2 seconds 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1188 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 13 sheets defined 7.3% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.691A pdb=" N ASP H 90 " --> pdb=" O THR H 87 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 87 through 91' Processing helix chain 'H' and resid 161 through 165 Processing helix chain 'I' and resid 385 through 390 removed outlier: 3.998A pdb=" N SER I 390 " --> pdb=" O PRO I 387 " (cutoff:3.500A) Processing helix chain 'I' and resid 395 through 399 Processing helix chain 'I' and resid 411 through 416 Processing helix chain 'I' and resid 431 through 435 removed outlier: 3.705A pdb=" N SER I 435 " --> pdb=" O ALA I 432 " (cutoff:3.500A) Processing helix chain 'I' and resid 449 through 453 removed outlier: 3.637A pdb=" N MET I 452 " --> pdb=" O PRO I 449 " (cutoff:3.500A) Processing helix chain 'I' and resid 524 through 528 removed outlier: 4.085A pdb=" N SER I 528 " --> pdb=" O PRO I 525 " (cutoff:3.500A) Processing helix chain 'K' and resid 80 through 84 removed outlier: 3.651A pdb=" N SER K 84 " --> pdb=" O PRO K 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.644A pdb=" N TYR H 94 " --> pdb=" O THR H 114 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 21 through 23 Processing sheet with id=AA3, first strand: chain 'H' and resid 143 through 145 Processing sheet with id=AA4, first strand: chain 'H' and resid 148 through 152 removed outlier: 4.636A pdb=" N LEU H 148 " --> pdb=" O SER H 187 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N SER H 187 " --> pdb=" O LEU H 148 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N LYS H 150 " --> pdb=" O LEU H 185 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LEU H 185 " --> pdb=" O LYS H 150 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TYR H 152 " --> pdb=" O TYR H 183 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 157 through 160 Processing sheet with id=AA6, first strand: chain 'I' and resid 400 through 404 removed outlier: 3.754A pdb=" N LYS I 400 " --> pdb=" O TYR I 445 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR I 445 " --> pdb=" O LYS I 400 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 408 through 409 Processing sheet with id=AA8, first strand: chain 'I' and resid 513 through 515 removed outlier: 3.699A pdb=" N TYR I 497 " --> pdb=" O VAL I 561 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N SER I 557 " --> pdb=" O ASN I 501 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 11 through 13 removed outlier: 5.677A pdb=" N LEU K 11 " --> pdb=" O GLU K 106 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 19 through 21 removed outlier: 3.795A pdb=" N ASP K 71 " --> pdb=" O SER K 68 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 49 through 50 Processing sheet with id=AB3, first strand: chain 'K' and resid 115 through 118 removed outlier: 3.613A pdb=" N SER K 163 " --> pdb=" O SER K 177 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 154 through 155 113 hydrogen bonds defined for protein. 233 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: 1.21 Time building geometry restraints manager: 1.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1055 1.33 - 1.45: 1105 1.45 - 1.57: 2753 1.57 - 1.69: 0 1.69 - 1.81: 26 Bond restraints: 4939 Sorted by residual: bond pdb=" C SER H 186 " pdb=" O SER H 186 " ideal model delta sigma weight residual 1.236 1.362 -0.126 1.21e-02 6.83e+03 1.08e+02 bond pdb=" C SER H 160 " pdb=" O SER H 160 " ideal model delta sigma weight residual 1.234 1.358 -0.124 1.22e-02 6.72e+03 1.03e+02 bond pdb=" N VAL H 191 " pdb=" CA VAL H 191 " ideal model delta sigma weight residual 1.457 1.493 -0.036 9.00e-03 1.23e+04 1.58e+01 bond pdb=" N VAL K 192 " pdb=" CA VAL K 192 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.15e-02 7.56e+03 1.30e+01 bond pdb=" N ILE K 59 " pdb=" CA ILE K 59 " ideal model delta sigma weight residual 1.460 1.492 -0.032 9.30e-03 1.16e+04 1.20e+01 ... (remaining 4934 not shown) Histogram of bond angle deviations from ideal: 99.45 - 106.42: 179 106.42 - 113.38: 2682 113.38 - 120.35: 1992 120.35 - 127.31: 1831 127.31 - 134.28: 48 Bond angle restraints: 6732 Sorted by residual: angle pdb=" O SER H 186 " pdb=" C SER H 186 " pdb=" CA ASER H 186 " ideal model delta sigma weight residual 120.38 132.17 -11.79 1.09e+00 8.42e-01 1.17e+02 angle pdb=" O SER H 186 " pdb=" C SER H 186 " pdb=" CA BSER H 186 " ideal model delta sigma weight residual 120.38 132.13 -11.75 1.09e+00 8.42e-01 1.16e+02 angle pdb=" O SER H 160 " pdb=" C SER H 160 " pdb=" CA ASER H 160 " ideal model delta sigma weight residual 120.92 133.26 -12.34 1.15e+00 7.56e-01 1.15e+02 angle pdb=" O SER H 160 " pdb=" C SER H 160 " pdb=" CA BSER H 160 " ideal model delta sigma weight residual 120.92 133.26 -12.34 1.15e+00 7.56e-01 1.15e+02 angle pdb=" CA ASER H 160 " pdb=" C SER H 160 " pdb=" N TRP H 161 " ideal model delta sigma weight residual 115.86 104.32 11.54 1.24e+00 6.50e-01 8.66e+01 ... (remaining 6727 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.15: 2626 16.15 - 32.30: 263 32.30 - 48.44: 69 48.44 - 64.59: 13 64.59 - 80.74: 9 Dihedral angle restraints: 2980 sinusoidal: 1121 harmonic: 1859 Sorted by residual: dihedral pdb=" CA GLU H 155 " pdb=" C GLU H 155 " pdb=" N PRO H 156 " pdb=" CA PRO H 156 " ideal model delta harmonic sigma weight residual 0.00 40.97 -40.97 0 5.00e+00 4.00e-02 6.71e+01 dihedral pdb=" CA ASN I 521 " pdb=" C ASN I 521 " pdb=" N GLN I 522 " pdb=" CA GLN I 522 " ideal model delta harmonic sigma weight residual 180.00 149.27 30.73 0 5.00e+00 4.00e-02 3.78e+01 dihedral pdb=" CA ASP K 61 " pdb=" C ASP K 61 " pdb=" N ARG K 62 " pdb=" CA ARG K 62 " ideal model delta harmonic sigma weight residual 180.00 149.99 30.01 0 5.00e+00 4.00e-02 3.60e+01 ... (remaining 2977 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 539 0.085 - 0.169: 186 0.169 - 0.254: 44 0.254 - 0.339: 2 0.339 - 0.423: 3 Chirality restraints: 774 Sorted by residual: chirality pdb=" CA GLN H 199 " pdb=" N GLN H 199 " pdb=" C GLN H 199 " pdb=" CB GLN H 199 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.48e+00 chirality pdb=" CA BSER H 186 " pdb=" N SER H 186 " pdb=" C SER H 186 " pdb=" CB BSER H 186 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.04e+00 chirality pdb=" CA ASER H 186 " pdb=" N SER H 186 " pdb=" C SER H 186 " pdb=" CB ASER H 186 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.01e+00 ... (remaining 771 not shown) Planarity restraints: 861 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN K 91 " 0.012 2.00e-02 2.50e+03 2.53e-02 6.39e+00 pdb=" C GLN K 91 " -0.044 2.00e-02 2.50e+03 pdb=" O GLN K 91 " 0.017 2.00e-02 2.50e+03 pdb=" N TYR K 92 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER H 160 " -0.039 2.00e-02 2.50e+03 2.27e-02 5.17e+00 pdb=" O SER H 160 " 0.016 2.00e-02 2.50e+03 pdb=" CA ASER H 160 " 0.012 2.00e-02 2.50e+03 pdb=" N TRP H 161 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER H 160 " -0.039 2.00e-02 2.50e+03 2.27e-02 5.17e+00 pdb=" O SER H 160 " 0.016 2.00e-02 2.50e+03 pdb=" CA BSER H 160 " 0.012 2.00e-02 2.50e+03 pdb=" N TRP H 161 " 0.012 2.00e-02 2.50e+03 ... (remaining 858 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 334 2.73 - 3.27: 4653 3.27 - 3.81: 7236 3.81 - 4.36: 9557 4.36 - 4.90: 15675 Nonbonded interactions: 37455 Sorted by model distance: nonbonded pdb=" O ASN I 521 " pdb=" N TYR I 523 " model vdw 2.186 2.520 nonbonded pdb=" O ALA H 121 " pdb=" OG SER H 122 " model vdw 2.260 2.440 nonbonded pdb=" OD1 ASN I 436 " pdb=" OH TYR I 438 " model vdw 2.268 2.440 nonbonded pdb=" O PRO I 463 " pdb=" ND2 ASN I 468 " model vdw 2.269 2.520 nonbonded pdb=" O LEU I 456 " pdb=" OG SER I 457 " model vdw 2.355 2.440 ... (remaining 37450 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=0.40 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: 1.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.380 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 17.870 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 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 : 0.011 0.126 4939 Z= 0.764 Angle : 1.460 12.344 6732 Z= 1.021 Chirality : 0.087 0.423 774 Planarity : 0.005 0.048 861 Dihedral : 14.527 80.739 1768 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 2.68 % Allowed : 16.22 % Favored : 81.10 % Rotamer: Outliers : 9.27 % Allowed : 6.18 % Favored : 84.55 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.33 % Twisted Proline : 2.63 % Twisted General : 0.33 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.21 (0.32), residues: 637 helix: -3.94 (0.94), residues: 12 sheet: -1.45 (0.34), residues: 249 loop : -2.65 (0.29), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP K 36 HIS 0.004 0.001 HIS K 199 PHE 0.013 0.002 PHE I 467 TYR 0.031 0.002 TYR I 438 ARG 0.005 0.001 ARG H 50 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 145 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 35 THR cc_start: 0.8196 (OUTLIER) cc_final: 0.7955 (m) REVERT: H 38 ARG cc_start: 0.8363 (ttp80) cc_final: 0.8024 (ttm-80) REVERT: H 157 VAL cc_start: 0.8806 (OUTLIER) cc_final: 0.8560 (p) REVERT: H 189 VAL cc_start: 0.5888 (OUTLIER) cc_final: 0.5675 (p) REVERT: I 438 TYR cc_start: 0.8187 (m-80) cc_final: 0.7809 (m-80) REVERT: I 502 LYS cc_start: 0.7873 (mtpp) cc_final: 0.7376 (mttp) REVERT: K 13 LEU cc_start: 0.7240 (OUTLIER) cc_final: 0.6634 (mt) REVERT: K 75 THR cc_start: 0.7424 (OUTLIER) cc_final: 0.6908 (p) REVERT: K 97 TRP cc_start: 0.7650 (m-10) cc_final: 0.7191 (m-10) REVERT: K 136 LEU cc_start: 0.8169 (tp) cc_final: 0.7959 (tt) outliers start: 51 outliers final: 14 residues processed: 174 average time/residue: 0.1780 time to fit residues: 38.3122 Evaluate side-chains 114 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 95 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 189 VAL Chi-restraints excluded: chain H residue 195 SER Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 111 VAL Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 148 GLN Chi-restraints excluded: chain K residue 164 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 53 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 25 optimal weight: 0.4980 chunk 49 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 36 optimal weight: 0.1980 chunk 57 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 486 HIS I 519 ASN I 582 ASN K 6 GLN K 38 GLN K 90 GLN K 125 GLN K 148 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4939 Z= 0.261 Angle : 0.740 11.142 6732 Z= 0.381 Chirality : 0.047 0.205 774 Planarity : 0.005 0.035 861 Dihedral : 8.482 51.214 715 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.47 % Allowed : 10.71 % Favored : 88.82 % Rotamer: Outliers : 6.00 % Allowed : 13.27 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.33 % 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: -2.90 (0.32), residues: 637 helix: -3.97 (1.01), residues: 12 sheet: -1.47 (0.33), residues: 262 loop : -2.24 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 97 HIS 0.002 0.001 HIS I 486 PHE 0.018 0.002 PHE I 423 TYR 0.020 0.002 TYR I 445 ARG 0.006 0.001 ARG K 62 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 94 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 502 LYS cc_start: 0.8035 (mtpp) cc_final: 0.7529 (mttp) REVERT: K 13 LEU cc_start: 0.7361 (OUTLIER) cc_final: 0.6716 (mt) REVERT: K 76 ILE cc_start: 0.7026 (mt) cc_final: 0.6583 (mt) REVERT: K 143 ARG cc_start: 0.6322 (mtp85) cc_final: 0.5931 (ttm-80) outliers start: 33 outliers final: 19 residues processed: 118 average time/residue: 0.1902 time to fit residues: 27.9185 Evaluate side-chains 100 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 80 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 62 GLN Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain I residue 417 LEU Chi-restraints excluded: chain I residue 426 SER Chi-restraints excluded: chain I residue 521 ASN Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 111 VAL Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain K residue 206 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 31 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 19 optimal weight: 0.0270 chunk 45 optimal weight: 2.9990 overall best weight: 0.8840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 171 HIS H 206 ASN I 486 HIS I 521 ASN K 90 GLN ** K 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 4939 Z= 0.343 Angle : 0.775 12.012 6732 Z= 0.396 Chirality : 0.049 0.210 774 Planarity : 0.005 0.038 861 Dihedral : 7.316 53.401 703 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.47 % Allowed : 12.44 % Favored : 87.09 % Rotamer: Outliers : 6.18 % Allowed : 17.82 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.33 % 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: -2.84 (0.32), residues: 637 helix: -4.73 (0.51), residues: 24 sheet: -1.23 (0.32), residues: 268 loop : -2.23 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 161 HIS 0.002 0.001 HIS I 486 PHE 0.020 0.002 PHE I 423 TYR 0.026 0.003 TYR H 183 ARG 0.007 0.001 ARG K 62 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 86 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 502 LYS cc_start: 0.7923 (mtpp) cc_final: 0.7470 (mttp) REVERT: K 76 ILE cc_start: 0.6924 (mt) cc_final: 0.6446 (mt) outliers start: 34 outliers final: 23 residues processed: 109 average time/residue: 0.1901 time to fit residues: 25.7029 Evaluate side-chains 102 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 79 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain I residue 417 LEU Chi-restraints excluded: chain I residue 426 SER Chi-restraints excluded: chain I residue 480 ILE Chi-restraints excluded: chain I residue 521 ASN Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 90 GLN Chi-restraints excluded: chain K residue 111 VAL Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 172 SER Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain K residue 206 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 56 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 6 optimal weight: 0.0980 chunk 27 optimal weight: 0.2980 chunk 38 optimal weight: 0.3980 chunk 57 optimal weight: 0.1980 chunk 60 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 overall best weight: 0.3180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 486 HIS K 90 GLN ** K 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4939 Z= 0.180 Angle : 0.664 10.016 6732 Z= 0.337 Chirality : 0.045 0.208 774 Planarity : 0.004 0.030 861 Dihedral : 6.617 53.880 701 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.47 % Allowed : 9.13 % Favored : 90.39 % Rotamer: Outliers : 4.36 % Allowed : 21.27 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.33 % 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: -2.60 (0.32), residues: 637 helix: -4.62 (0.54), residues: 24 sheet: -1.04 (0.32), residues: 268 loop : -2.09 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 36 HIS 0.001 0.000 HIS I 486 PHE 0.011 0.001 PHE I 423 TYR 0.018 0.002 TYR H 32 ARG 0.004 0.000 ARG K 62 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 82 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 157 VAL cc_start: 0.8845 (OUTLIER) cc_final: 0.8638 (p) REVERT: I 438 TYR cc_start: 0.8088 (m-80) cc_final: 0.7781 (m-80) REVERT: I 502 LYS cc_start: 0.8070 (mtpp) cc_final: 0.7628 (mttp) REVERT: K 13 LEU cc_start: 0.6438 (mt) cc_final: 0.6168 (mt) REVERT: K 76 ILE cc_start: 0.6836 (mt) cc_final: 0.6426 (mt) REVERT: K 124 GLU cc_start: 0.6833 (tm-30) cc_final: 0.6320 (tm-30) outliers start: 24 outliers final: 21 residues processed: 101 average time/residue: 0.1878 time to fit residues: 23.8899 Evaluate side-chains 99 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 77 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain I residue 405 THR Chi-restraints excluded: chain I residue 417 LEU Chi-restraints excluded: chain I residue 426 SER Chi-restraints excluded: chain I residue 530 VAL Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 90 GLN Chi-restraints excluded: chain K residue 111 VAL Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 172 SER Chi-restraints excluded: chain K residue 206 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 50 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 51 optimal weight: 0.2980 chunk 42 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 54 optimal weight: 0.0040 chunk 15 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 486 HIS K 38 GLN K 90 GLN ** K 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4939 Z= 0.211 Angle : 0.663 10.390 6732 Z= 0.333 Chirality : 0.045 0.182 774 Planarity : 0.004 0.027 861 Dihedral : 6.456 53.236 701 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.47 % Allowed : 10.71 % Favored : 88.82 % Rotamer: Outliers : 5.45 % Allowed : 20.73 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.33 % 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: -2.48 (0.32), residues: 637 helix: -4.59 (0.55), residues: 24 sheet: -0.88 (0.32), residues: 266 loop : -2.08 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 36 HIS 0.001 0.001 HIS I 486 PHE 0.012 0.001 PHE I 423 TYR 0.016 0.002 TYR H 32 ARG 0.003 0.000 ARG K 62 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 83 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 438 TYR cc_start: 0.8098 (m-80) cc_final: 0.7773 (m-80) REVERT: I 502 LYS cc_start: 0.8035 (mtpp) cc_final: 0.7570 (mttp) REVERT: K 76 ILE cc_start: 0.6850 (mt) cc_final: 0.6410 (mt) REVERT: K 124 GLU cc_start: 0.6788 (tm-30) cc_final: 0.6233 (tm-30) outliers start: 30 outliers final: 22 residues processed: 105 average time/residue: 0.1811 time to fit residues: 24.1773 Evaluate side-chains 102 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 80 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain I residue 405 THR Chi-restraints excluded: chain I residue 417 LEU Chi-restraints excluded: chain I residue 426 SER Chi-restraints excluded: chain I residue 521 ASN Chi-restraints excluded: chain I residue 530 VAL Chi-restraints excluded: chain K residue 90 GLN Chi-restraints excluded: chain K residue 111 VAL Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 153 ASN Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 172 SER Chi-restraints excluded: chain K residue 206 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 54 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 35 optimal weight: 0.0010 chunk 15 optimal weight: 0.1980 chunk 60 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 5 optimal weight: 0.1980 chunk 20 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 overall best weight: 0.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 486 HIS K 90 GLN ** K 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.3872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4939 Z= 0.185 Angle : 0.646 10.142 6732 Z= 0.322 Chirality : 0.044 0.179 774 Planarity : 0.004 0.028 861 Dihedral : 6.216 52.868 700 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.47 % Allowed : 9.61 % Favored : 89.92 % Rotamer: Outliers : 5.27 % Allowed : 21.09 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.33 % 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: -2.33 (0.33), residues: 637 helix: -3.91 (0.72), residues: 24 sheet: -0.69 (0.33), residues: 260 loop : -2.09 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 36 HIS 0.001 0.001 HIS I 486 PHE 0.011 0.001 PHE I 423 TYR 0.015 0.002 TYR H 32 ARG 0.003 0.000 ARG K 62 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 80 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 211 ASN cc_start: 0.6830 (m-40) cc_final: 0.6624 (t0) REVERT: I 502 LYS cc_start: 0.8076 (mtpp) cc_final: 0.7625 (mttp) REVERT: K 76 ILE cc_start: 0.6724 (OUTLIER) cc_final: 0.6282 (mt) REVERT: K 78 ARG cc_start: 0.4654 (tmt170) cc_final: 0.4168 (tpt170) REVERT: K 124 GLU cc_start: 0.6823 (tm-30) cc_final: 0.6301 (tm-30) outliers start: 29 outliers final: 24 residues processed: 102 average time/residue: 0.1774 time to fit residues: 23.2158 Evaluate side-chains 103 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 78 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain I residue 388 LEU Chi-restraints excluded: chain I residue 405 THR Chi-restraints excluded: chain I residue 417 LEU Chi-restraints excluded: chain I residue 426 SER Chi-restraints excluded: chain I residue 480 ILE Chi-restraints excluded: chain I residue 530 VAL Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 90 GLN Chi-restraints excluded: chain K residue 111 VAL Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 126 LEU Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 153 ASN Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 172 SER Chi-restraints excluded: chain K residue 206 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 6 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 51 optimal weight: 0.3980 chunk 60 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 36 optimal weight: 0.0040 chunk 18 optimal weight: 2.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 486 HIS K 90 GLN ** K 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.3971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4939 Z= 0.243 Angle : 0.686 13.531 6732 Z= 0.343 Chirality : 0.046 0.178 774 Planarity : 0.004 0.030 861 Dihedral : 6.309 52.288 700 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.47 % Allowed : 11.02 % Favored : 88.50 % Rotamer: Outliers : 5.45 % Allowed : 21.45 % Favored : 73.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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 (0.33), residues: 637 helix: -4.43 (0.70), residues: 18 sheet: -0.73 (0.33), residues: 260 loop : -2.01 (0.31), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 97 HIS 0.002 0.001 HIS K 199 PHE 0.013 0.001 PHE I 423 TYR 0.015 0.002 TYR H 32 ARG 0.004 0.000 ARG K 62 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 79 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 502 LYS cc_start: 0.8027 (mtpp) cc_final: 0.7574 (mttp) REVERT: K 76 ILE cc_start: 0.6759 (OUTLIER) cc_final: 0.6290 (mt) REVERT: K 124 GLU cc_start: 0.6835 (tm-30) cc_final: 0.6281 (tm-30) outliers start: 30 outliers final: 25 residues processed: 102 average time/residue: 0.1815 time to fit residues: 23.4848 Evaluate side-chains 104 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 78 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain I residue 388 LEU Chi-restraints excluded: chain I residue 405 THR Chi-restraints excluded: chain I residue 417 LEU Chi-restraints excluded: chain I residue 426 SER Chi-restraints excluded: chain I residue 480 ILE Chi-restraints excluded: chain I residue 530 VAL Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 90 GLN Chi-restraints excluded: chain K residue 111 VAL Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 126 LEU Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 153 ASN Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 172 SER Chi-restraints excluded: chain K residue 206 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 11 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 5 optimal weight: 0.0970 chunk 47 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 53 optimal weight: 0.0570 chunk 56 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 overall best weight: 0.4296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 486 HIS ** K 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.4102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4939 Z= 0.200 Angle : 0.659 13.309 6732 Z= 0.329 Chirality : 0.045 0.170 774 Planarity : 0.004 0.032 861 Dihedral : 6.170 52.486 700 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.47 % Allowed : 10.08 % Favored : 89.45 % Rotamer: Outliers : 5.27 % Allowed : 21.45 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.33 % 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 (0.33), residues: 637 helix: -4.01 (0.69), residues: 24 sheet: -0.60 (0.33), residues: 269 loop : -2.12 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 97 HIS 0.001 0.000 HIS K 199 PHE 0.013 0.001 PHE I 423 TYR 0.014 0.002 TYR H 32 ARG 0.003 0.000 ARG K 62 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 80 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 502 LYS cc_start: 0.8043 (mtpp) cc_final: 0.7593 (mttp) REVERT: K 76 ILE cc_start: 0.6694 (OUTLIER) cc_final: 0.6361 (mt) REVERT: K 78 ARG cc_start: 0.4609 (tmt170) cc_final: 0.4130 (tpt170) REVERT: K 124 GLU cc_start: 0.6821 (tm-30) cc_final: 0.6265 (tm-30) outliers start: 29 outliers final: 24 residues processed: 100 average time/residue: 0.1935 time to fit residues: 24.6908 Evaluate side-chains 101 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 76 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain I residue 388 LEU Chi-restraints excluded: chain I residue 405 THR Chi-restraints excluded: chain I residue 417 LEU Chi-restraints excluded: chain I residue 422 ASP Chi-restraints excluded: chain I residue 426 SER Chi-restraints excluded: chain I residue 480 ILE Chi-restraints excluded: chain I residue 530 VAL Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 111 VAL Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 153 ASN Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 172 SER Chi-restraints excluded: chain K residue 206 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 24 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 36 optimal weight: 0.4980 chunk 28 optimal weight: 0.5980 chunk 41 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 486 HIS K 90 GLN ** K 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.4213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4939 Z= 0.248 Angle : 0.694 13.538 6732 Z= 0.346 Chirality : 0.046 0.173 774 Planarity : 0.004 0.033 861 Dihedral : 6.309 52.545 700 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.47 % Allowed : 10.87 % Favored : 88.66 % Rotamer: Outliers : 5.27 % Allowed : 22.00 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.24 (0.33), residues: 637 helix: -4.46 (0.69), residues: 18 sheet: -0.66 (0.33), residues: 268 loop : -2.03 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 97 HIS 0.002 0.001 HIS K 199 PHE 0.014 0.002 PHE I 423 TYR 0.016 0.002 TYR H 183 ARG 0.004 0.000 ARG K 62 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 81 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 10 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7810 (mp0) REVERT: H 29 PHE cc_start: 0.8007 (OUTLIER) cc_final: 0.7655 (t80) REVERT: I 502 LYS cc_start: 0.8018 (mtpp) cc_final: 0.7565 (mttp) REVERT: K 76 ILE cc_start: 0.6748 (OUTLIER) cc_final: 0.6396 (mt) REVERT: K 78 ARG cc_start: 0.4625 (tmt170) cc_final: 0.4147 (tpt170) REVERT: K 124 GLU cc_start: 0.6951 (tm-30) cc_final: 0.6362 (tm-30) outliers start: 29 outliers final: 25 residues processed: 101 average time/residue: 0.1869 time to fit residues: 23.8532 Evaluate side-chains 107 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 79 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain I residue 388 LEU Chi-restraints excluded: chain I residue 405 THR Chi-restraints excluded: chain I residue 417 LEU Chi-restraints excluded: chain I residue 422 ASP Chi-restraints excluded: chain I residue 426 SER Chi-restraints excluded: chain I residue 480 ILE Chi-restraints excluded: chain I residue 486 HIS Chi-restraints excluded: chain I residue 530 VAL Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 90 GLN Chi-restraints excluded: chain K residue 111 VAL Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 153 ASN Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 172 SER Chi-restraints excluded: chain K residue 206 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 62 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 38 optimal weight: 0.0870 chunk 30 optimal weight: 0.8980 chunk 39 optimal weight: 0.3980 chunk 53 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 46 optimal weight: 0.0770 chunk 7 optimal weight: 1.9990 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 486 HIS K 90 GLN ** K 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.4299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4939 Z= 0.202 Angle : 0.671 13.231 6732 Z= 0.333 Chirality : 0.045 0.175 774 Planarity : 0.004 0.037 861 Dihedral : 6.164 52.988 700 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.47 % Allowed : 10.08 % Favored : 89.45 % Rotamer: Outliers : 5.09 % Allowed : 21.82 % Favored : 73.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.33 % 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: -2.22 (0.33), residues: 637 helix: -4.08 (0.67), residues: 24 sheet: -0.60 (0.33), residues: 269 loop : -2.03 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 97 HIS 0.001 0.000 HIS I 486 PHE 0.012 0.001 PHE I 423 TYR 0.017 0.002 TYR H 32 ARG 0.003 0.000 ARG K 62 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 76 time to evaluate : 0.552 Fit side-chains revert: symmetry clash REVERT: H 10 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7811 (mp0) REVERT: H 29 PHE cc_start: 0.7913 (OUTLIER) cc_final: 0.7625 (t80) REVERT: I 502 LYS cc_start: 0.8058 (mtpp) cc_final: 0.7613 (mttp) REVERT: K 76 ILE cc_start: 0.6685 (OUTLIER) cc_final: 0.6352 (mt) REVERT: K 78 ARG cc_start: 0.4653 (tmt170) cc_final: 0.4196 (tpt170) REVERT: K 124 GLU cc_start: 0.6921 (tm-30) cc_final: 0.6289 (tm-30) outliers start: 28 outliers final: 24 residues processed: 95 average time/residue: 0.1827 time to fit residues: 22.2875 Evaluate side-chains 103 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 76 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain I residue 388 LEU Chi-restraints excluded: chain I residue 405 THR Chi-restraints excluded: chain I residue 417 LEU Chi-restraints excluded: chain I residue 426 SER Chi-restraints excluded: chain I residue 480 ILE Chi-restraints excluded: chain I residue 486 HIS Chi-restraints excluded: chain I residue 530 VAL Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 111 VAL Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 153 ASN Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 172 SER Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 206 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 13 optimal weight: 0.0040 chunk 50 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 486 HIS K 90 GLN ** K 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.158890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.139796 restraints weight = 21622.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.144426 restraints weight = 13545.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.146786 restraints weight = 4994.611| |-----------------------------------------------------------------------------| r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3792 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3792 r_free = 0.3792 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3792 r_free = 0.3792 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3792 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.4319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4939 Z= 0.274 Angle : 0.710 13.597 6732 Z= 0.354 Chirality : 0.046 0.172 774 Planarity : 0.004 0.036 861 Dihedral : 6.330 54.276 700 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.47 % Allowed : 11.97 % Favored : 87.56 % Rotamer: Outliers : 5.27 % Allowed : 22.00 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.36 (0.32), residues: 637 helix: -4.50 (0.69), residues: 18 sheet: -0.75 (0.34), residues: 245 loop : -2.04 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 97 HIS 0.006 0.001 HIS I 486 PHE 0.014 0.002 PHE I 423 TYR 0.018 0.002 TYR H 183 ARG 0.004 0.000 ARG K 62 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1491.39 seconds wall clock time: 27 minutes 34.21 seconds (1654.21 seconds total)