Starting phenix.real_space_refine on Thu Feb 15 00:52:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8com_16777/02_2024/8com_16777.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8com_16777/02_2024/8com_16777.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8com_16777/02_2024/8com_16777.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8com_16777/02_2024/8com_16777.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8com_16777/02_2024/8com_16777.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8com_16777/02_2024/8com_16777.pdb" } resolution = 3.3 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= 0.001 sd= 0.076 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 254 5.49 5 S 18 5.16 5 C 5887 2.51 5 N 2043 2.21 5 O 2503 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 59": "OE1" <-> "OE2" Residue "E GLU 77": "OE1" <-> "OE2" Residue "G TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10705 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 710 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 3, 'TRANS': 87} Chain: "B" Number of atoms: 597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 597 Classifications: {'peptide': 76} Link IDs: {'TRANS': 75} Chain: "C" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 732 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "D" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "E" Number of atoms: 669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 669 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 2, 'TRANS': 82} Chain: "F" Number of atoms: 592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 592 Classifications: {'peptide': 75} Link IDs: {'TRANS': 74} Chain: "G" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 736 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "H" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "I" Number of atoms: 2620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 2620 Classifications: {'DNA': 127} Link IDs: {'rna3p': 126} Chain: "J" Number of atoms: 2587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 2587 Classifications: {'DNA': 127} Link IDs: {'rna3p': 126} Time building chain proxies: 6.15, per 1000 atoms: 0.57 Number of scatterers: 10705 At special positions: 0 Unit cell: (73.781, 116.06, 115.231, 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 18 16.00 P 254 15.00 O 2503 8.00 N 2043 7.00 C 5887 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: 6.04 Conformation dependent library (CDL) restraints added in 1.2 seconds 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1316 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 9 sheets defined 74.6% alpha, 2.5% beta 126 base pairs and 210 stacking pairs defined. Time for finding SS restraints: 5.30 Creating SS restraints... Processing helix chain 'A' and resid 42 through 53 removed outlier: 3.648A pdb=" N ARG A 53 " --> pdb=" O ARG A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 74 removed outlier: 3.589A pdb=" N ALA A 74 " --> pdb=" O GLU A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 111 removed outlier: 3.651A pdb=" N LEU A 87 " --> pdb=" O SER A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 129 Processing helix chain 'B' and resid 28 through 40 Processing helix chain 'B' and resid 47 through 74 removed outlier: 3.639A pdb=" N GLU B 51 " --> pdb=" O VAL B 47 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA B 69 " --> pdb=" O ARG B 65 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TYR B 70 " --> pdb=" O ASP B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 91 Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 27 through 38 Processing helix chain 'C' and resid 44 through 72 removed outlier: 3.629A pdb=" N ALA C 48 " --> pdb=" O GLY C 44 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLN C 72 " --> pdb=" O LYS C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 92 Processing helix chain 'C' and resid 93 through 99 Processing helix chain 'D' and resid 25 through 37 removed outlier: 3.624A pdb=" N ILE D 36 " --> pdb=" O SER D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 73 Processing helix chain 'D' and resid 78 through 90 Processing helix chain 'D' and resid 91 through 111 removed outlier: 3.846A pdb=" N HIS D 97 " --> pdb=" O ASP D 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 54 Processing helix chain 'E' and resid 60 through 76 Processing helix chain 'E' and resid 85 through 92 Processing helix chain 'E' and resid 92 through 111 removed outlier: 3.540A pdb=" N TYR E 96 " --> pdb=" O ALA E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 127 Processing helix chain 'F' and resid 28 through 40 Processing helix chain 'F' and resid 47 through 74 removed outlier: 3.734A pdb=" N GLU F 51 " --> pdb=" O VAL F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 92 Processing helix chain 'G' and resid 15 through 20 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 44 through 73 removed outlier: 3.603A pdb=" N ALA G 48 " --> pdb=" O GLY G 44 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 92 Processing helix chain 'G' and resid 94 through 99 Processing helix chain 'H' and resid 25 through 37 Processing helix chain 'H' and resid 43 through 72 Processing helix chain 'H' and resid 79 through 90 Processing helix chain 'H' and resid 91 through 111 removed outlier: 3.680A pdb=" N HIS H 97 " --> pdb=" O ASP H 93 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER H 111 " --> pdb=" O SER H 107 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 81 removed outlier: 7.234A pdb=" N ARG A 80 " --> pdb=" O VAL B 79 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 116 Processing sheet with id=AA3, first strand: chain 'B' and resid 95 through 96 Processing sheet with id=AA4, first strand: chain 'C' and resid 79 through 80 Processing sheet with id=AA5, first strand: chain 'C' and resid 103 through 104 removed outlier: 6.823A pdb=" N THR C 103 " --> pdb=" O TYR F 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 80 through 81 removed outlier: 8.289A pdb=" N ARG E 80 " --> pdb=" O VAL F 79 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 115 through 116 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.410A pdb=" N ARG G 42 " --> pdb=" O LEU H 77 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 79 through 80 385 hydrogen bonds defined for protein. 1155 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 327 hydrogen bonds 654 hydrogen bond angles 0 basepair planarities 126 basepair parallelities 210 stacking parallelities Total time for adding SS restraints: 3.83 Time building geometry restraints manager: 6.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2175 1.33 - 1.45: 3568 1.45 - 1.57: 5110 1.57 - 1.69: 506 1.69 - 1.81: 32 Bond restraints: 11391 Sorted by residual: bond pdb=" C4' DG I 20 " pdb=" C3' DG I 20 " ideal model delta sigma weight residual 1.523 1.546 -0.023 2.00e-02 2.50e+03 1.28e+00 bond pdb=" C3' DG I -21 " pdb=" O3' DG I -21 " ideal model delta sigma weight residual 1.422 1.455 -0.033 3.00e-02 1.11e+03 1.22e+00 bond pdb=" CA LYS C 76 " pdb=" C LYS C 76 " ideal model delta sigma weight residual 1.523 1.537 -0.014 1.34e-02 5.57e+03 1.08e+00 bond pdb=" CB GLU E 77 " pdb=" CG GLU E 77 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.04e+00 bond pdb=" C3' DT I -17 " pdb=" O3' DT I -17 " ideal model delta sigma weight residual 1.422 1.452 -0.030 3.00e-02 1.11e+03 1.03e+00 ... (remaining 11386 not shown) Histogram of bond angle deviations from ideal: 97.99 - 105.19: 1063 105.19 - 112.38: 6498 112.38 - 119.57: 3530 119.57 - 126.76: 4658 126.76 - 133.95: 716 Bond angle restraints: 16465 Sorted by residual: angle pdb=" N VAL C 27 " pdb=" CA VAL C 27 " pdb=" C VAL C 27 " ideal model delta sigma weight residual 113.47 108.61 4.86 1.01e+00 9.80e-01 2.31e+01 angle pdb=" CB MET H 47 " pdb=" CG MET H 47 " pdb=" SD MET H 47 " ideal model delta sigma weight residual 112.70 121.69 -8.99 3.00e+00 1.11e-01 8.99e+00 angle pdb=" CA LYS A 76 " pdb=" CB LYS A 76 " pdb=" CG LYS A 76 " ideal model delta sigma weight residual 114.10 119.84 -5.74 2.00e+00 2.50e-01 8.23e+00 angle pdb=" CA ASP H 56 " pdb=" CB ASP H 56 " pdb=" CG ASP H 56 " ideal model delta sigma weight residual 112.60 110.18 2.42 1.00e+00 1.00e+00 5.84e+00 angle pdb=" C3' DG J 9 " pdb=" C2' DG J 9 " pdb=" C1' DG J 9 " ideal model delta sigma weight residual 101.60 97.99 3.61 1.50e+00 4.44e-01 5.78e+00 ... (remaining 16460 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.04: 4650 30.04 - 60.09: 1493 60.09 - 90.13: 40 90.13 - 120.18: 1 120.18 - 150.22: 4 Dihedral angle restraints: 6188 sinusoidal: 4152 harmonic: 2036 Sorted by residual: dihedral pdb=" C4' DT I -17 " pdb=" C3' DT I -17 " pdb=" O3' DT I -17 " pdb=" P DT I -16 " ideal model delta sinusoidal sigma weight residual 220.00 69.78 150.22 1 3.50e+01 8.16e-04 1.46e+01 dihedral pdb=" C4' DC J 4 " pdb=" C3' DC J 4 " pdb=" O3' DC J 4 " pdb=" P DC J 5 " ideal model delta sinusoidal sigma weight residual 220.00 75.92 144.08 1 3.50e+01 8.16e-04 1.42e+01 dihedral pdb=" C4' DG I -21 " pdb=" C3' DG I -21 " pdb=" O3' DG I -21 " pdb=" P DC I -20 " ideal model delta sinusoidal sigma weight residual 220.00 94.78 125.22 1 3.50e+01 8.16e-04 1.24e+01 ... (remaining 6185 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1250 0.028 - 0.057: 495 0.057 - 0.085: 127 0.085 - 0.113: 23 0.113 - 0.142: 5 Chirality restraints: 1900 Sorted by residual: chirality pdb=" CG LEU E 127 " pdb=" CB LEU E 127 " pdb=" CD1 LEU E 127 " pdb=" CD2 LEU E 127 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 5.02e-01 chirality pdb=" CA ILE B 44 " pdb=" N ILE B 44 " pdb=" C ILE B 44 " pdb=" CB ILE B 44 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.01e-01 chirality pdb=" CA ILE F 27 " pdb=" N ILE F 27 " pdb=" C ILE F 27 " pdb=" CB ILE F 27 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.62e-01 ... (remaining 1897 not shown) Planarity restraints: 1198 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG I 20 " 0.023 2.00e-02 2.50e+03 1.11e-02 3.70e+00 pdb=" N9 DG I 20 " -0.029 2.00e-02 2.50e+03 pdb=" C8 DG I 20 " 0.003 2.00e-02 2.50e+03 pdb=" N7 DG I 20 " 0.000 2.00e-02 2.50e+03 pdb=" C5 DG I 20 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 20 " 0.002 2.00e-02 2.50e+03 pdb=" O6 DG I 20 " 0.005 2.00e-02 2.50e+03 pdb=" N1 DG I 20 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DG I 20 " 0.000 2.00e-02 2.50e+03 pdb=" N2 DG I 20 " -0.001 2.00e-02 2.50e+03 pdb=" N3 DG I 20 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DG I 20 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 28 " 0.012 2.00e-02 2.50e+03 1.23e-02 3.05e+00 pdb=" CG TYR H 28 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR H 28 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR H 28 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR H 28 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR H 28 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR H 28 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR H 28 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I -4 " 0.021 2.00e-02 2.50e+03 8.79e-03 2.32e+00 pdb=" N9 DG I -4 " -0.019 2.00e-02 2.50e+03 pdb=" C8 DG I -4 " -0.002 2.00e-02 2.50e+03 pdb=" N7 DG I -4 " -0.005 2.00e-02 2.50e+03 pdb=" C5 DG I -4 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG I -4 " 0.004 2.00e-02 2.50e+03 pdb=" O6 DG I -4 " 0.006 2.00e-02 2.50e+03 pdb=" N1 DG I -4 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DG I -4 " 0.001 2.00e-02 2.50e+03 pdb=" N2 DG I -4 " -0.005 2.00e-02 2.50e+03 pdb=" N3 DG I -4 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DG I -4 " -0.002 2.00e-02 2.50e+03 ... (remaining 1195 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1639 2.76 - 3.30: 9909 3.30 - 3.83: 21739 3.83 - 4.37: 24091 4.37 - 4.90: 35191 Nonbonded interactions: 92569 Sorted by model distance: nonbonded pdb=" OE1 GLU E 91 " pdb=" OH TYR F 98 " model vdw 2.228 2.440 nonbonded pdb=" OG SER E 54 " pdb=" OD1 ASP E 56 " model vdw 2.275 2.440 nonbonded pdb=" OH TYR B 73 " pdb=" OE2 GLU D 81 " model vdw 2.284 2.440 nonbonded pdb=" OD2 ASP D 56 " pdb=" OH TYR F 96 " model vdw 2.291 2.440 nonbonded pdb=" N LYS E 61 " pdb=" OP1 DG I 18 " model vdw 2.308 2.520 ... (remaining 92564 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 45 through 129) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 24 through 98) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 15 through 111) } ncs_group { reference = chain 'D' 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=1.00 max=1.00 mean=1.00 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: 1.310 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: 7.190 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 36.780 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.040 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 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 : 0.004 0.036 11391 Z= 0.204 Angle : 0.571 8.994 16465 Z= 0.346 Chirality : 0.032 0.142 1900 Planarity : 0.003 0.029 1198 Dihedral : 28.543 150.219 4872 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.34 % Allowed : 13.97 % Favored : 85.69 % 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: 2.02 (0.32), residues: 692 helix: 2.12 (0.23), residues: 510 sheet: None (None), residues: 0 loop : -0.96 (0.43), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 25 HIS 0.001 0.000 HIS D 97 PHE 0.011 0.002 PHE H 58 TYR 0.030 0.002 TYR H 28 ARG 0.004 0.000 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 79 time to evaluate : 0.859 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 79 average time/residue: 0.2418 time to fit residues: 27.1941 Evaluate side-chains 81 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 79 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 42 MET Chi-restraints excluded: chain E residue 94 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 76 optimal weight: 7.9990 chunk 68 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 71 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 11391 Z= 0.277 Angle : 0.595 8.497 16465 Z= 0.353 Chirality : 0.034 0.129 1900 Planarity : 0.004 0.039 1198 Dihedral : 31.293 150.059 3557 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.41 % Allowed : 13.10 % Favored : 84.48 % 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: 1.91 (0.32), residues: 692 helix: 2.03 (0.22), residues: 522 sheet: None (None), residues: 0 loop : -1.18 (0.45), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP H 25 HIS 0.002 0.000 HIS D 97 PHE 0.014 0.002 PHE A 64 TYR 0.028 0.002 TYR H 28 ARG 0.005 0.000 ARG D 80 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 87 time to evaluate : 0.863 Fit side-chains REVERT: A 76 LYS cc_start: 0.6927 (tmtt) cc_final: 0.6304 (tmtt) outliers start: 14 outliers final: 12 residues processed: 94 average time/residue: 0.2166 time to fit residues: 29.4253 Evaluate side-chains 92 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 80 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain H residue 86 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 45 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 68 optimal weight: 6.9990 chunk 56 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 82 optimal weight: 7.9990 chunk 89 optimal weight: 6.9990 chunk 73 optimal weight: 7.9990 chunk 28 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 81 optimal weight: 5.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11391 Z= 0.193 Angle : 0.543 8.111 16465 Z= 0.328 Chirality : 0.032 0.127 1900 Planarity : 0.003 0.040 1198 Dihedral : 30.997 149.491 3551 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 2.76 % Allowed : 14.31 % Favored : 82.93 % 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: 2.28 (0.32), residues: 692 helix: 2.30 (0.22), residues: 525 sheet: None (None), residues: 0 loop : -1.15 (0.46), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 25 HIS 0.002 0.000 HIS E 110 PHE 0.014 0.002 PHE A 64 TYR 0.018 0.002 TYR H 28 ARG 0.002 0.000 ARG A 46 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 84 time to evaluate : 0.813 Fit side-chains REVERT: A 76 LYS cc_start: 0.6938 (tmtt) cc_final: 0.6345 (tmtt) REVERT: F 90 LYS cc_start: 0.8244 (tmtt) cc_final: 0.7803 (tmtt) outliers start: 16 outliers final: 10 residues processed: 93 average time/residue: 0.2109 time to fit residues: 28.4843 Evaluate side-chains 90 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 80 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain H residue 86 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 62 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 87 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 73 optimal weight: 7.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11391 Z= 0.244 Angle : 0.562 8.978 16465 Z= 0.335 Chirality : 0.033 0.126 1900 Planarity : 0.003 0.039 1198 Dihedral : 31.161 149.458 3551 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 3.79 % Allowed : 14.83 % Favored : 81.38 % 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: 2.20 (0.32), residues: 692 helix: 2.24 (0.22), residues: 526 sheet: None (None), residues: 0 loop : -1.20 (0.45), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 25 HIS 0.001 0.000 HIS D 97 PHE 0.013 0.002 PHE A 64 TYR 0.016 0.002 TYR H 28 ARG 0.002 0.000 ARG A 46 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 82 time to evaluate : 0.837 Fit side-chains REVERT: A 76 LYS cc_start: 0.7007 (tmtt) cc_final: 0.6465 (tmtt) outliers start: 22 outliers final: 15 residues processed: 94 average time/residue: 0.2174 time to fit residues: 29.2105 Evaluate side-chains 97 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 82 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 86 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 75 optimal weight: 8.9990 chunk 60 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 11391 Z= 0.283 Angle : 0.589 9.475 16465 Z= 0.349 Chirality : 0.034 0.129 1900 Planarity : 0.003 0.039 1198 Dihedral : 31.272 151.188 3551 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 4.31 % Allowed : 15.52 % Favored : 80.17 % 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 (0.32), residues: 692 helix: 2.04 (0.22), residues: 526 sheet: None (None), residues: 0 loop : -1.25 (0.45), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 25 HIS 0.002 0.000 HIS E 110 PHE 0.014 0.002 PHE A 64 TYR 0.017 0.002 TYR H 28 ARG 0.003 0.000 ARG C 29 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 86 time to evaluate : 0.779 Fit side-chains revert: symmetry clash REVERT: H 83 GLN cc_start: 0.7447 (OUTLIER) cc_final: 0.7203 (tt0) outliers start: 25 outliers final: 19 residues processed: 99 average time/residue: 0.2413 time to fit residues: 33.1581 Evaluate side-chains 103 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 83 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 128 ARG Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 83 GLN Chi-restraints excluded: chain H residue 86 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 79 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 73 optimal weight: 7.9990 chunk 40 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 84 optimal weight: 6.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11391 Z= 0.238 Angle : 0.562 8.847 16465 Z= 0.335 Chirality : 0.033 0.131 1900 Planarity : 0.003 0.039 1198 Dihedral : 31.070 151.347 3551 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 4.48 % Allowed : 16.90 % Favored : 78.62 % 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: 2.08 (0.32), residues: 692 helix: 2.18 (0.22), residues: 526 sheet: None (None), residues: 0 loop : -1.33 (0.44), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP H 25 HIS 0.001 0.000 HIS E 110 PHE 0.014 0.002 PHE A 64 TYR 0.016 0.002 TYR G 50 ARG 0.005 0.000 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 83 time to evaluate : 1.218 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 21 residues processed: 97 average time/residue: 0.2758 time to fit residues: 38.3544 Evaluate side-chains 103 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 82 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 128 ARG Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 86 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 9 optimal weight: 0.0050 chunk 50 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 74 optimal weight: 8.9990 chunk 87 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11391 Z= 0.167 Angle : 0.530 7.974 16465 Z= 0.319 Chirality : 0.031 0.123 1900 Planarity : 0.003 0.039 1198 Dihedral : 30.831 151.087 3551 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 2.24 % Allowed : 19.48 % Favored : 78.28 % 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: 2.54 (0.32), residues: 692 helix: 2.51 (0.22), residues: 525 sheet: None (None), residues: 0 loop : -1.15 (0.46), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 25 HIS 0.001 0.000 HIS E 110 PHE 0.015 0.001 PHE A 64 TYR 0.014 0.002 TYR H 28 ARG 0.005 0.000 ARG B 25 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 93 time to evaluate : 0.823 Fit side-chains outliers start: 13 outliers final: 9 residues processed: 101 average time/residue: 0.2241 time to fit residues: 32.1111 Evaluate side-chains 91 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 82 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain H residue 86 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 26 optimal weight: 4.9990 chunk 17 optimal weight: 0.5980 chunk 16 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 79 optimal weight: 10.0000 chunk 84 optimal weight: 7.9990 chunk 76 optimal weight: 7.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 11391 Z= 0.354 Angle : 0.628 9.939 16465 Z= 0.365 Chirality : 0.036 0.192 1900 Planarity : 0.004 0.036 1198 Dihedral : 31.374 152.635 3551 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.79 % Allowed : 19.14 % Favored : 77.07 % 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 (0.32), residues: 692 helix: 1.93 (0.22), residues: 529 sheet: None (None), residues: 0 loop : -1.42 (0.45), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP H 25 HIS 0.002 0.001 HIS D 97 PHE 0.015 0.002 PHE E 64 TYR 0.015 0.002 TYR H 28 ARG 0.005 0.000 ARG B 25 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 85 time to evaluate : 0.944 Fit side-chains REVERT: A 76 LYS cc_start: 0.6978 (tmtt) cc_final: 0.6527 (tmtt) REVERT: D 47 MET cc_start: 0.8153 (tpp) cc_final: 0.7937 (tpp) outliers start: 22 outliers final: 15 residues processed: 95 average time/residue: 0.3102 time to fit residues: 40.0242 Evaluate side-chains 97 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 82 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain D residue 42 MET Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain H residue 86 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 81 optimal weight: 5.9990 chunk 84 optimal weight: 7.9990 chunk 49 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 chunk 64 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 73 optimal weight: 7.9990 chunk 77 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 11391 Z= 0.283 Angle : 0.591 9.217 16465 Z= 0.347 Chirality : 0.034 0.146 1900 Planarity : 0.003 0.036 1198 Dihedral : 31.199 152.676 3551 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.62 % Allowed : 19.14 % Favored : 77.24 % 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: 1.81 (0.32), residues: 692 helix: 1.98 (0.22), residues: 528 sheet: None (None), residues: 0 loop : -1.44 (0.45), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP H 25 HIS 0.001 0.000 HIS D 97 PHE 0.013 0.002 PHE A 64 TYR 0.017 0.002 TYR G 50 ARG 0.007 0.000 ARG B 25 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 80 time to evaluate : 0.919 Fit side-chains REVERT: A 76 LYS cc_start: 0.7001 (tmtt) cc_final: 0.6553 (tmtt) outliers start: 21 outliers final: 17 residues processed: 92 average time/residue: 0.2448 time to fit residues: 31.9457 Evaluate side-chains 95 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 78 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain D residue 42 MET Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 128 ARG Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain H residue 86 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 41 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 90 optimal weight: 7.9990 chunk 83 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 chunk 7 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 chunk 76 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11391 Z= 0.186 Angle : 0.553 8.366 16465 Z= 0.328 Chirality : 0.032 0.131 1900 Planarity : 0.003 0.036 1198 Dihedral : 31.020 152.978 3551 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.41 % Allowed : 20.34 % Favored : 77.24 % 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: 2.23 (0.32), residues: 692 helix: 2.30 (0.22), residues: 524 sheet: None (None), residues: 0 loop : -1.27 (0.45), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 25 HIS 0.001 0.000 HIS E 110 PHE 0.016 0.002 PHE A 64 TYR 0.015 0.002 TYR C 57 ARG 0.007 0.000 ARG B 25 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 85 time to evaluate : 0.810 Fit side-chains REVERT: A 76 LYS cc_start: 0.6989 (tmtt) cc_final: 0.6594 (tmtt) REVERT: C 39 TYR cc_start: 0.9336 (m-80) cc_final: 0.8963 (m-80) outliers start: 14 outliers final: 12 residues processed: 91 average time/residue: 0.2528 time to fit residues: 32.2076 Evaluate side-chains 94 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 82 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 128 ARG Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain H residue 86 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 66 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 72 optimal weight: 6.9990 chunk 30 optimal weight: 0.7980 chunk 74 optimal weight: 8.9990 chunk 9 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.172396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.124114 restraints weight = 14761.029| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 1.88 r_work: 0.3375 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11391 Z= 0.186 Angle : 0.550 8.057 16465 Z= 0.328 Chirality : 0.032 0.157 1900 Planarity : 0.003 0.036 1198 Dihedral : 31.010 152.642 3551 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 2.07 % Allowed : 20.52 % Favored : 77.41 % 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: 2.24 (0.32), residues: 692 helix: 2.28 (0.22), residues: 526 sheet: None (None), residues: 0 loop : -1.23 (0.46), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 25 HIS 0.001 0.000 HIS D 97 PHE 0.015 0.002 PHE A 64 TYR 0.015 0.002 TYR H 28 ARG 0.007 0.000 ARG B 25 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1958.91 seconds wall clock time: 36 minutes 18.63 seconds (2178.63 seconds total)