Starting phenix.real_space_refine on Sun Dec 10 12:37:22 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g8g_29850/12_2023/8g8g_29850.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g8g_29850/12_2023/8g8g_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_29850/12_2023/8g8g_29850.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g8g_29850/12_2023/8g8g_29850.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g8g_29850/12_2023/8g8g_29850.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g8g_29850/12_2023/8g8g_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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 7.83, 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: 7.90 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: 7.31 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: 6.98 Time building geometry restraints manager: 8.08 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: 0.760 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: 3.710 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 48.790 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.060 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.090 ------------------------------------------------------------------------------- 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 : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 0 residues processed: 273 average time/residue: 0.3217 time to fit residues: 120.7763 Evaluate side-chains 133 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 1.129 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3225 ------------------------------------------------------------------------------- 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 E 55 GLN ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6544 moved from start: 0.7230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.075 15521 Z= 0.431 Angle : 0.924 7.936 22435 Z= 0.525 Chirality : 0.048 0.220 2550 Planarity : 0.007 0.065 1630 Dihedral : 31.410 173.898 4949 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 19.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 4.46 % Allowed : 19.24 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.26), residues: 911 helix: 1.00 (0.19), residues: 661 sheet: None (None), residues: 0 loop : -1.52 (0.34), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP X 207 HIS 0.008 0.002 HIS F 75 PHE 0.017 0.002 PHE D 67 TYR 0.029 0.003 TYR E 41 ARG 0.014 0.001 ARG C 20 *********************** 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 164 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 129 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 13 residues processed: 153 average time/residue: 0.2971 time to fit residues: 64.5394 Evaluate side-chains 108 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 95 time to evaluate : 1.094 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1266 time to fit residues: 4.4207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 92 optimal weight: 40.0000 chunk 76 optimal weight: 10.0000 chunk 30 optimal weight: 4.9990 chunk 111 optimal weight: 50.0000 chunk 120 optimal weight: 40.0000 chunk 99 optimal weight: 7.9990 chunk 110 optimal weight: 8.9990 chunk 38 optimal weight: 0.9990 chunk 89 optimal weight: 8.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 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: 0.6926 moved from start: 1.0049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 15521 Z= 0.373 Angle : 0.733 7.690 22435 Z= 0.427 Chirality : 0.041 0.185 2550 Planarity : 0.006 0.049 1630 Dihedral : 31.294 179.694 4949 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.91 % Allowed : 20.00 % Favored : 78.09 % 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: 1.34 (0.27), residues: 911 helix: 1.78 (0.20), residues: 662 sheet: None (None), residues: 0 loop : -1.60 (0.34), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP X 277 HIS 0.016 0.002 HIS D 79 PHE 0.018 0.002 PHE A 67 TYR 0.037 0.003 TYR D 80 ARG 0.013 0.001 ARG D 27 *********************** 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 141 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 126 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 5 residues processed: 135 average time/residue: 0.3033 time to fit residues: 58.0000 Evaluate side-chains 107 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 102 time to evaluate : 1.152 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1390 time to fit residues: 2.6436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 9.9990 chunk 84 optimal weight: 7.9990 chunk 58 optimal weight: 0.4980 chunk 12 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 75 optimal weight: 10.0000 chunk 112 optimal weight: 6.9990 chunk 118 optimal weight: 8.9990 chunk 106 optimal weight: 8.9990 chunk 32 optimal weight: 0.9990 chunk 99 optimal weight: 7.9990 overall best weight: 3.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN D 81 ASN E 113 HIS ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 1.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 15521 Z= 0.316 Angle : 0.679 7.671 22435 Z= 0.400 Chirality : 0.038 0.143 2550 Planarity : 0.005 0.050 1630 Dihedral : 31.357 174.595 4949 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.04 % Allowed : 20.00 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.28), residues: 911 helix: 2.05 (0.20), residues: 663 sheet: None (None), residues: 0 loop : -1.73 (0.33), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP X 207 HIS 0.006 0.001 HIS B 75 PHE 0.014 0.002 PHE X 187 TYR 0.013 0.001 TYR B 88 ARG 0.005 0.001 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 134 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 118 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 4 residues processed: 129 average time/residue: 0.2995 time to fit residues: 54.5570 Evaluate side-chains 105 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 101 time to evaluate : 1.100 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2039 time to fit residues: 2.5715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 88 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 chunk 101 optimal weight: 6.9990 chunk 82 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 60 optimal weight: 9.9990 chunk 106 optimal weight: 8.9990 chunk 30 optimal weight: 6.9990 chunk 40 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN E 76 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: 0.7154 moved from start: 1.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 15521 Z= 0.368 Angle : 0.694 9.559 22435 Z= 0.407 Chirality : 0.039 0.155 2550 Planarity : 0.005 0.108 1630 Dihedral : 31.508 175.910 4949 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.68 % Allowed : 20.13 % Favored : 77.20 % 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: 1.54 (0.28), residues: 911 helix: 1.94 (0.20), residues: 666 sheet: None (None), residues: 0 loop : -1.64 (0.34), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP X 207 HIS 0.007 0.001 HIS B 75 PHE 0.014 0.002 PHE A 67 TYR 0.026 0.002 TYR B 88 ARG 0.006 0.001 ARG B 23 *********************** 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 136 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 115 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 11 residues processed: 129 average time/residue: 0.3156 time to fit residues: 57.3716 Evaluate side-chains 111 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 100 time to evaluate : 1.157 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1559 time to fit residues: 4.1606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 69 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 119 optimal weight: 40.0000 chunk 98 optimal weight: 7.9990 chunk 55 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 114 optimal weight: 8.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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** B 27 GLN ** X 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 1.2805 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= 0.207 Angle : 0.619 14.031 22435 Z= 0.365 Chirality : 0.034 0.131 2550 Planarity : 0.004 0.041 1630 Dihedral : 31.208 175.037 4949 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.25 % Allowed : 21.02 % Favored : 78.73 % 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: 1.90 (0.28), residues: 911 helix: 2.23 (0.20), residues: 666 sheet: None (None), residues: 0 loop : -1.60 (0.34), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP X 207 HIS 0.005 0.001 HIS B 75 PHE 0.011 0.001 PHE X 187 TYR 0.049 0.002 TYR B 88 ARG 0.004 0.000 ARG E 42 *********************** 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 118 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 116 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 118 average time/residue: 0.3015 time to fit residues: 51.0903 Evaluate side-chains 107 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 1.077 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 86 optimal weight: 8.9990 chunk 100 optimal weight: 8.9990 chunk 66 optimal weight: 9.9990 chunk 118 optimal weight: 9.9990 chunk 74 optimal weight: 6.9990 chunk 72 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 47 optimal weight: 7.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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** B 27 GLN E 108 ASN ** X 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 1.2984 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= 0.210 Angle : 0.608 11.370 22435 Z= 0.361 Chirality : 0.034 0.126 2550 Planarity : 0.004 0.041 1630 Dihedral : 31.042 174.759 4949 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.51 % Allowed : 22.55 % 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: 1.95 (0.28), residues: 911 helix: 2.25 (0.20), residues: 666 sheet: None (None), residues: 0 loop : -1.54 (0.34), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP X 207 HIS 0.006 0.001 HIS B 75 PHE 0.012 0.001 PHE X 194 TYR 0.034 0.001 TYR D 80 ARG 0.002 0.000 ARG C 20 *********************** 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 116 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 112 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 113 average time/residue: 0.2998 time to fit residues: 48.9585 Evaluate side-chains 106 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 105 time to evaluate : 1.172 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1343 time to fit residues: 1.6000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 7.9990 chunk 35 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 75 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 58 optimal weight: 4.9990 chunk 11 optimal weight: 9.9990 chunk 93 optimal weight: 20.0000 chunk 107 optimal weight: 10.0000 chunk 113 optimal weight: 5.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- 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** B 27 GLN E 108 ASN F 75 HIS ** X 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 1.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 15521 Z= 0.299 Angle : 0.647 11.438 22435 Z= 0.380 Chirality : 0.036 0.147 2550 Planarity : 0.004 0.041 1630 Dihedral : 31.319 175.479 4949 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.51 % Allowed : 22.93 % Favored : 76.56 % 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: 1.76 (0.28), residues: 911 helix: 2.07 (0.20), residues: 667 sheet: None (None), residues: 0 loop : -1.49 (0.34), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP X 277 HIS 0.011 0.001 HIS B 75 PHE 0.009 0.001 PHE G 25 TYR 0.031 0.002 TYR D 80 ARG 0.005 0.000 ARG A 116 *********************** 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 114 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 110 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 112 average time/residue: 0.3087 time to fit residues: 49.9972 Evaluate side-chains 106 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 105 time to evaluate : 1.336 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1723 time to fit residues: 1.6300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 8.9990 chunk 110 optimal weight: 40.0000 chunk 113 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 86 optimal weight: 8.9990 chunk 33 optimal weight: 6.9990 chunk 99 optimal weight: 8.9990 chunk 104 optimal weight: 9.9990 chunk 72 optimal weight: 3.9990 chunk 116 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 1.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 15521 Z= 0.312 Angle : 0.649 11.087 22435 Z= 0.382 Chirality : 0.036 0.148 2550 Planarity : 0.004 0.043 1630 Dihedral : 31.217 174.848 4949 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.51 % Allowed : 23.18 % Favored : 76.31 % 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: 1.77 (0.28), residues: 911 helix: 2.09 (0.20), residues: 667 sheet: None (None), residues: 0 loop : -1.50 (0.34), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP X 277 HIS 0.006 0.001 HIS B 75 PHE 0.008 0.001 PHE D 67 TYR 0.027 0.002 TYR D 80 ARG 0.003 0.000 ARG B 39 *********************** 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 109 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 105 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 109 average time/residue: 0.3207 time to fit residues: 49.5829 Evaluate side-chains 101 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 1.184 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 8.9990 chunk 55 optimal weight: 5.9990 chunk 81 optimal weight: 7.9990 chunk 122 optimal weight: 5.9990 chunk 112 optimal weight: 9.9990 chunk 97 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 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: 5.3990 ------------------------------------------------------------------------------- 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** F 93 GLN G 24 GLN H 44 GLN ** X 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 1.4201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 15521 Z= 0.394 Angle : 0.698 11.260 22435 Z= 0.407 Chirality : 0.039 0.151 2550 Planarity : 0.005 0.043 1630 Dihedral : 31.564 175.579 4949 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.38 % Allowed : 23.57 % Favored : 76.05 % 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: 1.51 (0.28), residues: 911 helix: 1.86 (0.20), residues: 667 sheet: None (None), residues: 0 loop : -1.48 (0.34), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP X 207 HIS 0.006 0.001 HIS B 75 PHE 0.009 0.002 PHE G 25 TYR 0.034 0.002 TYR D 80 ARG 0.004 0.000 ARG A 116 ********************** 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 108 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 105 time to evaluate : 1.111 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 107 average time/residue: 0.3126 time to fit residues: 47.4149 Evaluate side-chains 101 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 100 time to evaluate : 1.143 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1301 time to fit residues: 1.5898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 8.9990 chunk 89 optimal weight: 8.9990 chunk 14 optimal weight: 0.9980 chunk 27 optimal weight: 0.0370 chunk 97 optimal weight: 10.0000 chunk 40 optimal weight: 8.9990 chunk 100 optimal weight: 7.9990 chunk 12 optimal weight: 0.0980 chunk 18 optimal weight: 1.9990 chunk 85 optimal weight: 8.9990 chunk 5 optimal weight: 7.9990 overall best weight: 2.2262 ------------------------------------------------------------------------------- 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 108 ASN ** X 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 218 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 = 0.3592 r_free = 0.3592 target = 0.059521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.032558 restraints weight = 93297.290| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 3.30 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 1.4250 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= 0.226 Angle : 0.641 11.087 22435 Z= 0.378 Chirality : 0.035 0.164 2550 Planarity : 0.004 0.043 1630 Dihedral : 31.170 174.876 4949 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.00 % Allowed : 23.95 % Favored : 76.05 % 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: 1.72 (0.28), residues: 911 helix: 2.02 (0.21), residues: 667 sheet: None (None), residues: 0 loop : -1.42 (0.35), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP X 207 HIS 0.007 0.001 HIS B 75 PHE 0.009 0.001 PHE X 175 TYR 0.021 0.001 TYR D 80 ARG 0.002 0.000 ARG B 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2479.81 seconds wall clock time: 46 minutes 0.31 seconds (2760.31 seconds total)