Starting phenix.real_space_refine on Sat Mar 16 10:59:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g8g_29850/03_2024/8g8g_29850.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g8g_29850/03_2024/8g8g_29850.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g8g_29850/03_2024/8g8g_29850.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g8g_29850/03_2024/8g8g_29850.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g8g_29850/03_2024/8g8g_29850.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g8g_29850/03_2024/8g8g_29850.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 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 P 348 5.49 5 S 17 5.16 5 C 8089 2.51 5 N 2711 2.21 5 O 3393 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 94": "OE1" <-> "OE2" Residue "A GLU 97": "OE1" <-> "OE2" Residue "A GLU 105": "OE1" <-> "OE2" Residue "A GLU 133": "OE1" <-> "OE2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "B GLU 53": "OE1" <-> "OE2" Residue "B GLU 63": "OE1" <-> "OE2" Residue "B GLU 74": "OE1" <-> "OE2" Residue "C GLU 91": "OE1" <-> "OE2" Residue "D GLU 68": "OE1" <-> "OE2" Residue "D GLU 73": "OE1" <-> "OE2" Residue "D GLU 90": "OE1" <-> "OE2" Residue "E GLU 73": "OE1" <-> "OE2" Residue "E GLU 94": "OE1" <-> "OE2" Residue "E GLU 97": "OE1" <-> "OE2" Residue "F GLU 53": "OE1" <-> "OE2" Residue "G GLU 41": "OE1" <-> "OE2" Residue "G GLU 61": "OE1" <-> "OE2" Residue "G GLU 64": "OE1" <-> "OE2" Residue "H GLU 68": "OE1" <-> "OE2" Residue "H GLU 102": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14558 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 895 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "B" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 657 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 756 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "E" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 668 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "G" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 915 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 5, 'TRANS': 113} Chain: "H" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 3539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 3539 Classifications: {'DNA': 174} Link IDs: {'rna3p': 173} Chain: "J" Number of atoms: 3595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 3595 Classifications: {'DNA': 174} Link IDs: {'rna3p': 173} Chain: "X" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1152 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain breaks: 1 Time building chain proxies: 7.85, per 1000 atoms: 0.54 Number of scatterers: 14558 At special positions: 0 Unit cell: (97.52, 116.6, 189.74, 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 17 16.00 P 348 15.00 O 3393 8.00 N 2711 7.00 C 8089 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 7.58 Conformation dependent library (CDL) restraints added in 1.5 seconds 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1752 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 10 sheets defined 71.5% alpha, 2.6% beta 157 base pairs and 325 stacking pairs defined. Time for finding SS restraints: 7.67 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.335A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 removed outlier: 3.572A pdb=" N GLN D 44 " --> pdb=" O LYS D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 122 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.220A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 removed outlier: 3.537A pdb=" N LYS G 95 " --> pdb=" O GLU G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 122 Processing helix chain 'X' and resid 141 through 161 Processing helix chain 'X' and resid 163 through 176 Processing helix chain 'X' and resid 180 through 189 removed outlier: 3.554A pdb=" N ILE X 184 " --> pdb=" O SER X 180 " (cutoff:3.500A) Processing helix chain 'X' and resid 193 through 211 Proline residue: X 202 - end of helix Processing helix chain 'X' and resid 215 through 220 Processing helix chain 'X' and resid 238 through 249 Processing helix chain 'X' and resid 256 through 268 removed outlier: 3.681A pdb=" N HIS X 262 " --> pdb=" O GLN X 258 " (cutoff:3.500A) Processing helix chain 'X' and resid 270 through 288 removed outlier: 4.058A pdb=" N SER X 288 " --> pdb=" O LYS X 284 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.873A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.630A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.964A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.919A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.035A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 493 hydrogen bonds defined for protein. 1458 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 379 hydrogen bonds 758 hydrogen bond angles 0 basepair planarities 157 basepair parallelities 325 stacking parallelities Total time for adding SS restraints: 6.58 Time building geometry restraints manager: 8.07 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: 2787 1.33 - 1.45: 5064 1.45 - 1.57: 6948 1.57 - 1.69: 694 1.69 - 1.81: 28 Bond restraints: 15521 Sorted by residual: bond pdb=" C LEU G 116 " pdb=" N PRO G 117 " ideal model delta sigma weight residual 1.332 1.213 0.119 1.34e-02 5.57e+03 7.87e+01 bond pdb=" C LEU F 22 " pdb=" N ARG F 23 " ideal model delta sigma weight residual 1.330 1.384 -0.054 1.22e-02 6.72e+03 1.98e+01 bond pdb=" N ASN B 25 " pdb=" CA ASN B 25 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.23e-02 6.61e+03 7.35e+00 bond pdb=" N ILE B 26 " pdb=" CA ILE B 26 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.24e-02 6.50e+03 6.55e+00 bond pdb=" C ARG A 40 " pdb=" N TYR A 41 " ideal model delta sigma weight residual 1.329 1.356 -0.027 1.43e-02 4.89e+03 3.66e+00 ... (remaining 15516 not shown) Histogram of bond angle deviations from ideal: 97.56 - 104.85: 1375 104.85 - 112.13: 8743 112.13 - 119.42: 4715 119.42 - 126.71: 6487 126.71 - 133.99: 1115 Bond angle restraints: 22435 Sorted by residual: angle pdb=" CB MET X 197 " pdb=" CG MET X 197 " pdb=" SD MET X 197 " ideal model delta sigma weight residual 112.70 124.60 -11.90 3.00e+00 1.11e-01 1.57e+01 angle pdb=" CA GLU X 238 " pdb=" CB GLU X 238 " pdb=" CG GLU X 238 " ideal model delta sigma weight residual 114.10 120.63 -6.53 2.00e+00 2.50e-01 1.07e+01 angle pdb=" O3' DA I 74 " pdb=" C3' DA I 74 " pdb=" C2' DA I 74 " ideal model delta sigma weight residual 111.50 116.28 -4.78 1.50e+00 4.44e-01 1.02e+01 angle pdb=" CB LYS A 37 " pdb=" CG LYS A 37 " pdb=" CD LYS A 37 " ideal model delta sigma weight residual 111.30 117.84 -6.54 2.30e+00 1.89e-01 8.09e+00 angle pdb=" C3' DT J -88 " pdb=" C2' DT J -88 " pdb=" C1' DT J -88 " ideal model delta sigma weight residual 101.60 97.56 4.04 1.50e+00 4.44e-01 7.25e+00 ... (remaining 22430 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 6918 35.91 - 71.82: 1652 71.82 - 107.73: 18 107.73 - 143.64: 2 143.64 - 179.55: 1 Dihedral angle restraints: 8591 sinusoidal: 5887 harmonic: 2704 Sorted by residual: dihedral pdb=" C4' DC I 20 " pdb=" C3' DC I 20 " pdb=" O3' DC I 20 " pdb=" P DT I 21 " ideal model delta sinusoidal sigma weight residual 220.00 40.45 179.55 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG J -93 " pdb=" C3' DG J -93 " pdb=" O3' DG J -93 " pdb=" P DG J -92 " ideal model delta sinusoidal sigma weight residual 220.00 81.86 138.14 1 3.50e+01 8.16e-04 1.37e+01 dihedral pdb=" C4' DA I 52 " pdb=" C3' DA I 52 " pdb=" O3' DA I 52 " pdb=" P DA I 53 " ideal model delta sinusoidal sigma weight residual 220.00 84.27 135.73 1 3.50e+01 8.16e-04 1.34e+01 ... (remaining 8588 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2008 0.038 - 0.076: 454 0.076 - 0.114: 74 0.114 - 0.152: 12 0.152 - 0.190: 2 Chirality restraints: 2550 Sorted by residual: chirality pdb=" CA ILE B 26 " pdb=" N ILE B 26 " pdb=" C ILE B 26 " pdb=" CB ILE B 26 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 9.03e-01 chirality pdb=" CG LEU X 190 " pdb=" CB LEU X 190 " pdb=" CD1 LEU X 190 " pdb=" CD2 LEU X 190 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.83e-01 chirality pdb=" CA LEU X 267 " pdb=" N LEU X 267 " pdb=" C LEU X 267 " pdb=" CB LEU X 267 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.14 2.00e-01 2.50e+01 4.58e-01 ... (remaining 2547 not shown) Planarity restraints: 1630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU F 22 " 0.022 2.00e-02 2.50e+03 4.48e-02 2.00e+01 pdb=" C LEU F 22 " -0.077 2.00e-02 2.50e+03 pdb=" O LEU F 22 " 0.030 2.00e-02 2.50e+03 pdb=" N ARG F 23 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG E 42 " 0.033 5.00e-02 4.00e+02 4.98e-02 3.98e+00 pdb=" N PRO E 43 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO E 43 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO E 43 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 40 " 0.009 2.00e-02 2.50e+03 1.78e-02 3.17e+00 pdb=" C ARG A 40 " -0.031 2.00e-02 2.50e+03 pdb=" O ARG A 40 " 0.011 2.00e-02 2.50e+03 pdb=" N TYR A 41 " 0.010 2.00e-02 2.50e+03 ... (remaining 1627 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.28: 7 2.28 - 2.93: 5418 2.93 - 3.59: 21629 3.59 - 4.24: 41392 4.24 - 4.90: 59753 Nonbonded interactions: 128199 Sorted by model distance: nonbonded pdb=" O SER G 123 " pdb=" OP1 DG J -75 " model vdw 1.622 3.040 nonbonded pdb=" CD LYS G 124 " pdb=" O3' DA J -76 " model vdw 1.932 3.440 nonbonded pdb=" C SER G 123 " pdb=" OP1 DG J -75 " model vdw 2.057 3.270 nonbonded pdb=" NH1 ARG A 26 " pdb=" OP1 DA J 2 " model vdw 2.165 2.520 nonbonded pdb=" O HIS F 75 " pdb=" NH2 ARG H 89 " model vdw 2.238 2.520 ... (remaining 128194 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 38 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 20 through 101) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 11 through 118) } ncs_group { reference = (chain 'D' and resid 28 through 122) selection = chain 'H' } 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=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.590 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: 0.020 Extract box with map and model: 3.780 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 47.860 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.050 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4882 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.119 15521 Z= 0.278 Angle : 0.593 11.899 22435 Z= 0.354 Chirality : 0.033 0.190 2550 Planarity : 0.004 0.050 1630 Dihedral : 27.409 179.553 6839 Min Nonbonded Distance : 1.622 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.64 % Allowed : 14.27 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.25), residues: 911 helix: 0.14 (0.19), residues: 648 sheet: None (None), residues: 0 loop : -1.29 (0.33), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP X 277 HIS 0.004 0.001 HIS D 106 PHE 0.011 0.001 PHE X 187 TYR 0.009 0.001 TYR G 57 ARG 0.004 0.001 ARG E 42 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 271 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.5202 (mt) cc_final: 0.4916 (mt) REVERT: F 19 ARG cc_start: 0.7805 (mtt-85) cc_final: 0.7445 (ptp-170) REVERT: F 20 LYS cc_start: 0.7435 (tppt) cc_final: 0.7206 (tppt) outliers start: 5 outliers final: 0 residues processed: 273 average time/residue: 0.3115 time to fit residues: 116.4637 Evaluate side-chains 135 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 8.9990 chunk 93 optimal weight: 20.0000 chunk 51 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 chunk 62 optimal weight: 0.1980 chunk 49 optimal weight: 3.9990 chunk 96 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 71 optimal weight: 7.9990 chunk 111 optimal weight: 10.0000 overall best weight: 4.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN C 112 GLN E 55 GLN E 76 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 HIS H 81 ASN ** X 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6435 moved from start: 0.6466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.107 15521 Z= 0.409 Angle : 0.886 8.325 22435 Z= 0.500 Chirality : 0.046 0.239 2550 Planarity : 0.007 0.090 1630 Dihedral : 31.183 174.530 4949 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 18.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 4.33 % Allowed : 20.25 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.26), residues: 911 helix: 1.07 (0.19), residues: 661 sheet: None (None), residues: 0 loop : -1.45 (0.34), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP X 277 HIS 0.006 0.002 HIS B 75 PHE 0.016 0.002 PHE H 62 TYR 0.025 0.002 TYR H 37 ARG 0.017 0.001 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 131 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 19 ARG cc_start: 0.7725 (mtt-85) cc_final: 0.7272 (ptp-170) REVERT: G 91 GLU cc_start: 0.6966 (pm20) cc_final: 0.6387 (pm20) outliers start: 34 outliers final: 13 residues processed: 156 average time/residue: 0.2911 time to fit residues: 64.4820 Evaluate side-chains 110 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 97 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain X residue 158 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 92 optimal weight: 50.0000 chunk 76 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 111 optimal weight: 50.0000 chunk 120 optimal weight: 50.0000 chunk 99 optimal weight: 8.9990 chunk 110 optimal weight: 6.9990 chunk 38 optimal weight: 0.9980 chunk 89 optimal weight: 10.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN E 76 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6835 moved from start: 0.9213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 15521 Z= 0.356 Angle : 0.725 7.320 22435 Z= 0.425 Chirality : 0.039 0.220 2550 Planarity : 0.005 0.053 1630 Dihedral : 31.067 178.877 4949 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.42 % Allowed : 20.89 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.27), residues: 911 helix: 1.63 (0.20), residues: 662 sheet: None (None), residues: 0 loop : -1.48 (0.34), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP X 277 HIS 0.006 0.001 HIS E 113 PHE 0.019 0.002 PHE A 67 TYR 0.063 0.002 TYR B 88 ARG 0.011 0.001 ARG D 76 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 121 time to evaluate : 1.225 Fit side-chains revert: symmetry clash REVERT: B 59 LYS cc_start: 0.7541 (mtpt) cc_final: 0.6941 (mtpt) REVERT: H 48 ASP cc_start: 0.7505 (p0) cc_final: 0.7216 (p0) outliers start: 19 outliers final: 7 residues processed: 133 average time/residue: 0.2999 time to fit residues: 56.2250 Evaluate side-chains 101 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 94 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain X residue 158 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 20.0000 chunk 84 optimal weight: 8.9990 chunk 58 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 53 optimal weight: 8.9990 chunk 75 optimal weight: 10.0000 chunk 112 optimal weight: 5.9990 chunk 118 optimal weight: 8.9990 chunk 106 optimal weight: 8.9990 chunk 32 optimal weight: 0.9980 chunk 99 optimal weight: 7.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 1.0615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 15521 Z= 0.310 Angle : 0.661 7.091 22435 Z= 0.390 Chirality : 0.037 0.180 2550 Planarity : 0.005 0.041 1630 Dihedral : 31.141 176.597 4949 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.17 % Allowed : 21.91 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.27), residues: 911 helix: 1.99 (0.20), residues: 662 sheet: None (None), residues: 0 loop : -1.58 (0.34), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP X 277 HIS 0.008 0.002 HIS B 75 PHE 0.013 0.002 PHE D 67 TYR 0.037 0.002 TYR B 88 ARG 0.009 0.000 ARG D 76 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 113 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 HIS cc_start: 0.7788 (OUTLIER) cc_final: 0.7559 (t-90) REVERT: B 22 LEU cc_start: 0.4777 (OUTLIER) cc_final: 0.4106 (mm) REVERT: E 120 MET cc_start: 0.7740 (mmm) cc_final: 0.7081 (mtt) REVERT: H 48 ASP cc_start: 0.7627 (p0) cc_final: 0.7392 (p0) outliers start: 17 outliers final: 5 residues processed: 124 average time/residue: 0.3058 time to fit residues: 53.2880 Evaluate side-chains 103 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 96 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain G residue 100 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 0.9990 chunk 1 optimal weight: 0.3980 chunk 88 optimal weight: 10.0000 chunk 49 optimal weight: 0.9990 chunk 101 optimal weight: 6.9990 chunk 82 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 60 optimal weight: 8.9990 chunk 106 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 chunk 40 optimal weight: 8.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** X 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 1.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 15521 Z= 0.267 Angle : 0.643 8.201 22435 Z= 0.380 Chirality : 0.036 0.133 2550 Planarity : 0.005 0.071 1630 Dihedral : 31.052 175.943 4949 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.80 % Allowed : 20.25 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.28), residues: 911 helix: 2.12 (0.20), residues: 666 sheet: None (None), residues: 0 loop : -1.51 (0.35), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP X 207 HIS 0.005 0.001 HIS E 113 PHE 0.013 0.001 PHE A 67 TYR 0.063 0.002 TYR B 88 ARG 0.007 0.001 ARG D 76 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 115 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 48 ASP cc_start: 0.7407 (p0) cc_final: 0.7186 (p0) REVERT: X 283 GLN cc_start: 0.1022 (OUTLIER) cc_final: 0.0465 (tt0) outliers start: 22 outliers final: 12 residues processed: 130 average time/residue: 0.3049 time to fit residues: 56.3850 Evaluate side-chains 109 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 96 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain E residue 42 ARG Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain X residue 283 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 119 optimal weight: 7.9990 chunk 98 optimal weight: 8.9990 chunk 55 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN ** X 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 1.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15521 Z= 0.205 Angle : 0.603 9.648 22435 Z= 0.360 Chirality : 0.034 0.142 2550 Planarity : 0.004 0.045 1630 Dihedral : 30.921 175.252 4949 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.66 % Allowed : 21.66 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.28), residues: 911 helix: 2.31 (0.20), residues: 666 sheet: None (None), residues: 0 loop : -1.43 (0.34), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP X 207 HIS 0.005 0.001 HIS B 75 PHE 0.015 0.001 PHE X 194 TYR 0.059 0.002 TYR B 88 ARG 0.004 0.000 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 111 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 48 ASP cc_start: 0.7381 (p0) cc_final: 0.7161 (p0) outliers start: 13 outliers final: 7 residues processed: 120 average time/residue: 0.2918 time to fit residues: 50.0372 Evaluate side-chains 106 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 99 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain G residue 111 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 10.0000 chunk 67 optimal weight: 6.9990 chunk 86 optimal weight: 8.9990 chunk 100 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 chunk 118 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 72 optimal weight: 2.9990 chunk 54 optimal weight: 8.9990 chunk 73 optimal weight: 6.9990 chunk 47 optimal weight: 0.9980 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 HIS F 93 GLN ** X 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 1.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 15521 Z= 0.351 Angle : 0.679 11.246 22435 Z= 0.394 Chirality : 0.038 0.201 2550 Planarity : 0.005 0.051 1630 Dihedral : 31.422 175.574 4949 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.78 % Allowed : 22.55 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.28), residues: 911 helix: 2.14 (0.20), residues: 666 sheet: None (None), residues: 0 loop : -1.40 (0.35), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP X 277 HIS 0.006 0.001 HIS E 113 PHE 0.013 0.002 PHE X 187 TYR 0.079 0.002 TYR B 88 ARG 0.007 0.000 ARG D 76 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 104 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.7635 (tppp) cc_final: 0.7187 (ttmm) REVERT: H 48 ASP cc_start: 0.7456 (p0) cc_final: 0.7237 (p0) outliers start: 14 outliers final: 12 residues processed: 116 average time/residue: 0.2928 time to fit residues: 48.3060 Evaluate side-chains 110 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 98 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 123 SER Chi-restraints excluded: chain H residue 105 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 6.9990 chunk 35 optimal weight: 0.2980 chunk 23 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 75 optimal weight: 10.0000 chunk 80 optimal weight: 8.9990 chunk 58 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 93 optimal weight: 20.0000 chunk 107 optimal weight: 10.0000 chunk 113 optimal weight: 5.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 1.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15521 Z= 0.225 Angle : 0.612 9.321 22435 Z= 0.364 Chirality : 0.034 0.131 2550 Planarity : 0.004 0.041 1630 Dihedral : 31.082 174.819 4949 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.40 % Allowed : 23.69 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.28), residues: 911 helix: 2.30 (0.20), residues: 666 sheet: None (None), residues: 0 loop : -1.37 (0.35), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP X 207 HIS 0.004 0.001 HIS D 79 PHE 0.008 0.001 PHE A 67 TYR 0.064 0.002 TYR B 88 ARG 0.006 0.000 ARG C 20 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 106 time to evaluate : 1.132 Fit side-chains revert: symmetry clash REVERT: H 48 ASP cc_start: 0.7347 (p0) cc_final: 0.7131 (p0) outliers start: 11 outliers final: 7 residues processed: 116 average time/residue: 0.2755 time to fit residues: 46.6219 Evaluate side-chains 109 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 102 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain G residue 123 SER Chi-restraints excluded: chain H residue 86 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 10.0000 chunk 110 optimal weight: 6.9990 chunk 113 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 86 optimal weight: 8.9990 chunk 33 optimal weight: 6.9990 chunk 99 optimal weight: 8.9990 chunk 104 optimal weight: 10.0000 chunk 72 optimal weight: 0.8980 chunk 116 optimal weight: 6.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 1.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 15521 Z= 0.390 Angle : 0.694 11.413 22435 Z= 0.406 Chirality : 0.039 0.186 2550 Planarity : 0.005 0.041 1630 Dihedral : 31.516 175.713 4949 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.78 % Allowed : 23.57 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.28), residues: 911 helix: 1.99 (0.20), residues: 667 sheet: None (None), residues: 0 loop : -1.39 (0.35), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP X 207 HIS 0.007 0.002 HIS D 79 PHE 0.010 0.002 PHE A 67 TYR 0.074 0.002 TYR B 88 ARG 0.005 0.000 ARG B 67 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 104 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 48 ASP cc_start: 0.7489 (p0) cc_final: 0.7272 (p0) outliers start: 14 outliers final: 12 residues processed: 118 average time/residue: 0.2971 time to fit residues: 49.5773 Evaluate side-chains 110 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 98 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 123 SER Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 105 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 chunk 122 optimal weight: 7.9990 chunk 112 optimal weight: 40.0000 chunk 97 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 75 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 chunk 77 optimal weight: 10.0000 chunk 103 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 1.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 15521 Z= 0.347 Angle : 0.670 10.977 22435 Z= 0.393 Chirality : 0.037 0.148 2550 Planarity : 0.004 0.042 1630 Dihedral : 31.291 174.881 4949 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.66 % Allowed : 23.69 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.28), residues: 911 helix: 2.03 (0.20), residues: 667 sheet: None (None), residues: 0 loop : -1.38 (0.35), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP X 277 HIS 0.010 0.001 HIS B 75 PHE 0.009 0.002 PHE A 67 TYR 0.061 0.002 TYR B 88 ARG 0.005 0.000 ARG D 76 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 105 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 48 ASP cc_start: 0.7461 (p0) cc_final: 0.7239 (p0) outliers start: 13 outliers final: 13 residues processed: 117 average time/residue: 0.2958 time to fit residues: 49.6592 Evaluate side-chains 111 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 98 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 123 SER Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 105 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 1.9990 chunk 89 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 97 optimal weight: 10.0000 chunk 40 optimal weight: 4.9990 chunk 100 optimal weight: 8.9990 chunk 12 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 85 optimal weight: 10.0000 chunk 5 optimal weight: 0.0050 overall best weight: 1.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 HIS ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 283 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 = 0.3623 r_free = 0.3623 target = 0.060718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.033768 restraints weight = 92431.904| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 3.33 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 1.3933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15521 Z= 0.193 Angle : 0.633 10.948 22435 Z= 0.373 Chirality : 0.034 0.140 2550 Planarity : 0.004 0.044 1630 Dihedral : 30.873 174.442 4949 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.38 % Allowed : 25.22 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.28), residues: 911 helix: 2.18 (0.20), residues: 667 sheet: None (None), residues: 0 loop : -1.32 (0.35), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP X 207 HIS 0.005 0.001 HIS D 79 PHE 0.009 0.001 PHE E 67 TYR 0.019 0.001 TYR B 88 ARG 0.004 0.000 ARG A 116 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2527.41 seconds wall clock time: 46 minutes 24.19 seconds (2784.19 seconds total)