Starting phenix.real_space_refine on Sat Apr 6 11:10:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kgl_37225/04_2024/8kgl_37225.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kgl_37225/04_2024/8kgl_37225.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kgl_37225/04_2024/8kgl_37225.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kgl_37225/04_2024/8kgl_37225.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kgl_37225/04_2024/8kgl_37225.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kgl_37225/04_2024/8kgl_37225.pdb" } resolution = 4.3 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= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 24 5.16 5 C 5210 2.51 5 N 1386 2.21 5 O 1464 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 744": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 785": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 710": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 744": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 785": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 923": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 8084 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 4042 Classifications: {'peptide': 492} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 468} Chain: "B" Number of atoms: 4042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 4042 Classifications: {'peptide': 492} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 468} Time building chain proxies: 4.28, per 1000 atoms: 0.53 Number of scatterers: 8084 At special positions: 0 Unit cell: (150.15, 79.95, 108.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 24 16.00 O 1464 8.00 N 1386 7.00 C 5210 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: 2.76 Conformation dependent library (CDL) restraints added in 1.3 seconds 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1868 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 10 sheets defined 51.3% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 701 through 707 Processing helix chain 'A' and resid 715 through 729 Processing helix chain 'A' and resid 737 through 749 Processing helix chain 'A' and resid 754 through 765 Processing helix chain 'A' and resid 806 through 814 removed outlier: 4.926A pdb=" N THR A 812 " --> pdb=" O GLU A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 820 removed outlier: 3.620A pdb=" N TRP A 820 " --> pdb=" O GLU A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 830 removed outlier: 4.176A pdb=" N GLY A 829 " --> pdb=" O PHE A 826 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 846 removed outlier: 3.709A pdb=" N ILE A 845 " --> pdb=" O PRO A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 877 Processing helix chain 'A' and resid 882 through 893 Processing helix chain 'A' and resid 942 through 951 Processing helix chain 'A' and resid 981 through 990 removed outlier: 3.741A pdb=" N ARG A 985 " --> pdb=" O ASN A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1003 Processing helix chain 'A' and resid 1027 through 1070 removed outlier: 3.639A pdb=" N ILE A1031 " --> pdb=" O THR A1027 " (cutoff:3.500A) Proline residue: A1037 - end of helix Processing helix chain 'A' and resid 1070 through 1075 Processing helix chain 'A' and resid 1081 through 1092 Processing helix chain 'A' and resid 1098 through 1104 Processing helix chain 'A' and resid 1109 through 1116 Processing helix chain 'A' and resid 1122 through 1126 Processing helix chain 'A' and resid 1134 through 1159 removed outlier: 3.664A pdb=" N LYS A1138 " --> pdb=" O LEU A1134 " (cutoff:3.500A) Processing helix chain 'A' and resid 1166 through 1186 Processing helix chain 'B' and resid 702 through 707 Processing helix chain 'B' and resid 715 through 729 Processing helix chain 'B' and resid 737 through 749 Processing helix chain 'B' and resid 754 through 766 Processing helix chain 'B' and resid 806 through 814 removed outlier: 4.990A pdb=" N THR B 812 " --> pdb=" O GLU B 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 820 removed outlier: 3.637A pdb=" N TRP B 820 " --> pdb=" O GLU B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 842 through 846 removed outlier: 3.725A pdb=" N ILE B 845 " --> pdb=" O PRO B 842 " (cutoff:3.500A) Processing helix chain 'B' and resid 865 through 877 Processing helix chain 'B' and resid 882 through 893 Processing helix chain 'B' and resid 942 through 951 Processing helix chain 'B' and resid 981 through 990 removed outlier: 3.845A pdb=" N ARG B 985 " --> pdb=" O ASN B 981 " (cutoff:3.500A) Processing helix chain 'B' and resid 997 through 1003 Processing helix chain 'B' and resid 1027 through 1070 removed outlier: 3.684A pdb=" N ILE B1031 " --> pdb=" O THR B1027 " (cutoff:3.500A) Proline residue: B1037 - end of helix Processing helix chain 'B' and resid 1070 through 1075 Processing helix chain 'B' and resid 1081 through 1092 removed outlier: 3.523A pdb=" N ALA B1085 " --> pdb=" O ASP B1081 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N HIS B1092 " --> pdb=" O ILE B1088 " (cutoff:3.500A) Processing helix chain 'B' and resid 1098 through 1104 removed outlier: 3.522A pdb=" N ILE B1102 " --> pdb=" O ASN B1098 " (cutoff:3.500A) Processing helix chain 'B' and resid 1109 through 1116 Processing helix chain 'B' and resid 1122 through 1126 Processing helix chain 'B' and resid 1130 through 1133 removed outlier: 3.538A pdb=" N LEU B1133 " --> pdb=" O ALA B1130 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1130 through 1133' Processing helix chain 'B' and resid 1134 through 1159 removed outlier: 4.051A pdb=" N LYS B1138 " --> pdb=" O LEU B1134 " (cutoff:3.500A) Processing helix chain 'B' and resid 1166 through 1188 Processing sheet with id=AA1, first strand: chain 'A' and resid 779 through 782 Processing sheet with id=AA2, first strand: chain 'A' and resid 849 through 851 Processing sheet with id=AA3, first strand: chain 'A' and resid 909 through 913 Processing sheet with id=AA4, first strand: chain 'A' and resid 923 through 926 Processing sheet with id=AA5, first strand: chain 'A' and resid 1014 through 1016 Processing sheet with id=AA6, first strand: chain 'B' and resid 779 through 782 Processing sheet with id=AA7, first strand: chain 'B' and resid 849 through 851 Processing sheet with id=AA8, first strand: chain 'B' and resid 909 through 913 Processing sheet with id=AA9, first strand: chain 'B' and resid 923 through 926 Processing sheet with id=AB1, first strand: chain 'B' and resid 1014 through 1016 382 hydrogen bonds defined for protein. 1077 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.10 Time building geometry restraints manager: 3.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2396 1.34 - 1.45: 1439 1.45 - 1.57: 4409 1.57 - 1.69: 0 1.69 - 1.81: 42 Bond restraints: 8286 Sorted by residual: bond pdb=" C TYR A 776 " pdb=" N PRO A 777 " ideal model delta sigma weight residual 1.332 1.310 0.022 1.12e-02 7.97e+03 3.71e+00 bond pdb=" N ARG B1131 " pdb=" CA ARG B1131 " ideal model delta sigma weight residual 1.457 1.482 -0.024 1.35e-02 5.49e+03 3.23e+00 bond pdb=" CA GLN A1129 " pdb=" C GLN A1129 " ideal model delta sigma weight residual 1.523 1.547 -0.023 1.34e-02 5.57e+03 3.05e+00 bond pdb=" CB TRP A1170 " pdb=" CG TRP A1170 " ideal model delta sigma weight residual 1.498 1.445 0.053 3.10e-02 1.04e+03 2.93e+00 bond pdb=" CB TRP B1170 " pdb=" CG TRP B1170 " ideal model delta sigma weight residual 1.498 1.445 0.053 3.10e-02 1.04e+03 2.93e+00 ... (remaining 8281 not shown) Histogram of bond angle deviations from ideal: 97.97 - 105.18: 164 105.18 - 112.38: 4119 112.38 - 119.59: 2793 119.59 - 126.80: 4029 126.80 - 134.01: 99 Bond angle restraints: 11204 Sorted by residual: angle pdb=" N SER B1127 " pdb=" CA SER B1127 " pdb=" C SER B1127 " ideal model delta sigma weight residual 112.34 122.94 -10.60 1.30e+00 5.92e-01 6.65e+01 angle pdb=" N SER A1127 " pdb=" CA SER A1127 " pdb=" C SER A1127 " ideal model delta sigma weight residual 110.80 123.32 -12.52 2.13e+00 2.20e-01 3.45e+01 angle pdb=" N GLY A 786 " pdb=" CA GLY A 786 " pdb=" C GLY A 786 " ideal model delta sigma weight residual 110.56 116.02 -5.46 1.36e+00 5.41e-01 1.61e+01 angle pdb=" N ARG B1131 " pdb=" CA ARG B1131 " pdb=" C ARG B1131 " ideal model delta sigma weight residual 112.87 117.52 -4.65 1.20e+00 6.94e-01 1.50e+01 angle pdb=" N ASN B 851 " pdb=" CA ASN B 851 " pdb=" C ASN B 851 " ideal model delta sigma weight residual 108.23 114.45 -6.22 1.62e+00 3.81e-01 1.47e+01 ... (remaining 11199 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.17: 4406 11.17 - 22.35: 500 22.35 - 33.52: 63 33.52 - 44.69: 25 44.69 - 55.86: 4 Dihedral angle restraints: 4998 sinusoidal: 2088 harmonic: 2910 Sorted by residual: dihedral pdb=" CA GLN B1129 " pdb=" C GLN B1129 " pdb=" N ALA B1130 " pdb=" CA ALA B1130 " ideal model delta harmonic sigma weight residual -180.00 -124.14 -55.86 0 5.00e+00 4.00e-02 1.25e+02 dihedral pdb=" CA ILE A1125 " pdb=" C ILE A1125 " pdb=" N LEU A1126 " pdb=" CA LEU A1126 " ideal model delta harmonic sigma weight residual 180.00 -135.47 -44.53 0 5.00e+00 4.00e-02 7.93e+01 dihedral pdb=" CA LEU B1126 " pdb=" C LEU B1126 " pdb=" N SER B1127 " pdb=" CA SER B1127 " ideal model delta harmonic sigma weight residual -180.00 -135.95 -44.05 0 5.00e+00 4.00e-02 7.76e+01 ... (remaining 4995 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 791 0.046 - 0.092: 296 0.092 - 0.139: 94 0.139 - 0.185: 14 0.185 - 0.231: 5 Chirality restraints: 1200 Sorted by residual: chirality pdb=" CA SER B1127 " pdb=" N SER B1127 " pdb=" C SER B1127 " pdb=" CB SER B1127 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CB ILE B1023 " pdb=" CA ILE B1023 " pdb=" CG1 ILE B1023 " pdb=" CG2 ILE B1023 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CB ILE A1023 " pdb=" CA ILE A1023 " pdb=" CG1 ILE A1023 " pdb=" CG2 ILE A1023 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 1197 not shown) Planarity restraints: 1432 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B1170 " 0.031 2.00e-02 2.50e+03 3.18e-02 2.53e+01 pdb=" CG TRP B1170 " -0.084 2.00e-02 2.50e+03 pdb=" CD1 TRP B1170 " 0.045 2.00e-02 2.50e+03 pdb=" CD2 TRP B1170 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B1170 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP B1170 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B1170 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP B1170 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B1170 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP B1170 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A1170 " -0.030 2.00e-02 2.50e+03 3.09e-02 2.39e+01 pdb=" CG TRP A1170 " 0.082 2.00e-02 2.50e+03 pdb=" CD1 TRP A1170 " -0.043 2.00e-02 2.50e+03 pdb=" CD2 TRP A1170 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A1170 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP A1170 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A1170 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1170 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1170 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A1170 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B1129 " 0.016 2.00e-02 2.50e+03 3.19e-02 1.02e+01 pdb=" C GLN B1129 " -0.055 2.00e-02 2.50e+03 pdb=" O GLN B1129 " 0.021 2.00e-02 2.50e+03 pdb=" N ALA B1130 " 0.018 2.00e-02 2.50e+03 ... (remaining 1429 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2152 2.80 - 3.33: 7635 3.33 - 3.85: 13569 3.85 - 4.38: 15627 4.38 - 4.90: 24977 Nonbonded interactions: 63960 Sorted by model distance: nonbonded pdb=" OH TYR B1043 " pdb=" OE1 GLU B1173 " model vdw 2.276 2.440 nonbonded pdb=" OH TYR A1043 " pdb=" OE1 GLU A1173 " model vdw 2.277 2.440 nonbonded pdb=" O PHE B 809 " pdb=" OG1 THR B 812 " model vdw 2.279 2.440 nonbonded pdb=" O PHE A 809 " pdb=" OG1 THR A 812 " model vdw 2.280 2.440 nonbonded pdb=" OG SER A 787 " pdb=" OD2 ASP A 794 " model vdw 2.292 2.440 ... (remaining 63955 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' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.700 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: 10.130 Check model and map are aligned: 0.190 Set scattering table: 0.110 Process input model: 23.100 Find NCS groups from input model: 0.360 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 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 : 0.007 0.055 8286 Z= 0.463 Angle : 1.064 12.515 11204 Z= 0.596 Chirality : 0.054 0.231 1200 Planarity : 0.009 0.073 1432 Dihedral : 9.436 55.861 3130 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.85 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.21 (0.24), residues: 980 helix: -1.63 (0.19), residues: 436 sheet: -2.45 (0.49), residues: 112 loop : -2.47 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.084 0.007 TRP B1170 HIS 0.007 0.002 HIS B 752 PHE 0.024 0.003 PHE B 750 TYR 0.032 0.003 TYR B 917 ARG 0.008 0.001 ARG B 940 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 843 LEU cc_start: 0.9058 (tp) cc_final: 0.8791 (tt) REVERT: A 847 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7361 (mt-10) REVERT: A 954 SER cc_start: 0.8457 (m) cc_final: 0.8253 (p) REVERT: A 957 MET cc_start: 0.9455 (mmm) cc_final: 0.9068 (mmm) REVERT: A 966 TYR cc_start: 0.6365 (m-80) cc_final: 0.6058 (m-80) REVERT: A 1106 GLU cc_start: 0.8215 (pm20) cc_final: 0.7934 (pm20) REVERT: A 1169 VAL cc_start: 0.9403 (t) cc_final: 0.9083 (t) REVERT: B 843 LEU cc_start: 0.9001 (tp) cc_final: 0.8741 (tt) REVERT: B 847 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7092 (mt-10) REVERT: B 897 LEU cc_start: 0.7919 (mt) cc_final: 0.7414 (mp) REVERT: B 954 SER cc_start: 0.8554 (m) cc_final: 0.8350 (p) REVERT: B 957 MET cc_start: 0.9477 (mmm) cc_final: 0.9085 (mmm) REVERT: B 966 TYR cc_start: 0.6621 (m-80) cc_final: 0.6228 (m-80) REVERT: B 1106 GLU cc_start: 0.8184 (pm20) cc_final: 0.7917 (pm20) REVERT: B 1132 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7549 (tp30) REVERT: B 1148 MET cc_start: 0.7242 (mtm) cc_final: 0.6627 (ptm) REVERT: B 1169 VAL cc_start: 0.9387 (t) cc_final: 0.9036 (t) outliers start: 0 outliers final: 0 residues processed: 203 average time/residue: 0.2459 time to fit residues: 64.5600 Evaluate side-chains 107 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.8980 chunk 74 optimal weight: 20.0000 chunk 41 optimal weight: 0.9990 chunk 25 optimal weight: 20.0000 chunk 50 optimal weight: 0.8980 chunk 39 optimal weight: 0.0870 chunk 76 optimal weight: 8.9990 chunk 29 optimal weight: 7.9990 chunk 46 optimal weight: 0.9980 chunk 57 optimal weight: 8.9990 chunk 88 optimal weight: 1.9990 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 789 HIS ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1012 HIS ** A1075 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 789 HIS B 804 GLN ** B 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1012 HIS ** B1075 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8286 Z= 0.167 Angle : 0.589 8.752 11204 Z= 0.319 Chirality : 0.041 0.147 1200 Planarity : 0.006 0.050 1432 Dihedral : 6.493 46.024 1104 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.85 % 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: -1.67 (0.26), residues: 980 helix: 0.26 (0.24), residues: 428 sheet: -2.10 (0.46), residues: 122 loop : -2.23 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP A1170 HIS 0.004 0.001 HIS A 883 PHE 0.006 0.001 PHE A1094 TYR 0.014 0.002 TYR B 917 ARG 0.008 0.000 ARG B 716 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 714 MET cc_start: 0.8209 (mpp) cc_final: 0.7668 (mpp) REVERT: A 957 MET cc_start: 0.9461 (mmm) cc_final: 0.9065 (mmm) REVERT: A 966 TYR cc_start: 0.6342 (m-80) cc_final: 0.6118 (m-80) REVERT: A 1128 LEU cc_start: 0.8807 (mt) cc_final: 0.8567 (mt) REVERT: A 1169 VAL cc_start: 0.9285 (t) cc_final: 0.9038 (p) REVERT: B 714 MET cc_start: 0.8310 (mpp) cc_final: 0.7737 (mpp) REVERT: B 957 MET cc_start: 0.9466 (mmm) cc_final: 0.9072 (mmm) REVERT: B 966 TYR cc_start: 0.6584 (m-80) cc_final: 0.6289 (m-80) REVERT: B 1148 MET cc_start: 0.7165 (mtm) cc_final: 0.6627 (ttp) REVERT: B 1169 VAL cc_start: 0.9293 (t) cc_final: 0.8997 (p) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.2131 time to fit residues: 46.6102 Evaluate side-chains 98 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 20.0000 chunk 27 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 chunk 60 optimal weight: 0.6980 chunk 24 optimal weight: 0.2980 chunk 89 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 79 optimal weight: 10.0000 chunk 88 optimal weight: 1.9990 chunk 30 optimal weight: 8.9990 chunk 71 optimal weight: 10.0000 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 774 HIS ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1075 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 774 HIS ** B 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1075 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1099 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8286 Z= 0.185 Angle : 0.579 8.339 11204 Z= 0.312 Chirality : 0.041 0.151 1200 Planarity : 0.005 0.051 1432 Dihedral : 6.090 45.664 1104 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.85 % 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: -1.05 (0.27), residues: 980 helix: 0.90 (0.24), residues: 436 sheet: -1.81 (0.46), residues: 122 loop : -2.10 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A1170 HIS 0.005 0.001 HIS B1099 PHE 0.014 0.001 PHE A 710 TYR 0.019 0.002 TYR B 769 ARG 0.007 0.000 ARG B1039 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 714 MET cc_start: 0.8430 (mpp) cc_final: 0.7843 (mpp) REVERT: A 856 TRP cc_start: 0.4260 (p-90) cc_final: 0.3900 (p-90) REVERT: A 957 MET cc_start: 0.9483 (mmm) cc_final: 0.9073 (mmm) REVERT: A 966 TYR cc_start: 0.6286 (m-80) cc_final: 0.6081 (m-80) REVERT: A 1023 ILE cc_start: 0.9025 (tt) cc_final: 0.8741 (mm) REVERT: A 1148 MET cc_start: 0.7106 (ptt) cc_final: 0.5959 (ptt) REVERT: A 1169 VAL cc_start: 0.9341 (t) cc_final: 0.8679 (t) REVERT: B 714 MET cc_start: 0.8441 (mpp) cc_final: 0.7842 (mpp) REVERT: B 885 LEU cc_start: 0.8994 (mm) cc_final: 0.8778 (mt) REVERT: B 905 ASN cc_start: 0.8604 (m110) cc_final: 0.8264 (m110) REVERT: B 957 MET cc_start: 0.9473 (mmm) cc_final: 0.9070 (mmm) REVERT: B 966 TYR cc_start: 0.6559 (m-80) cc_final: 0.6277 (m-80) REVERT: B 1148 MET cc_start: 0.7221 (mtm) cc_final: 0.6890 (ttm) REVERT: B 1169 VAL cc_start: 0.9295 (t) cc_final: 0.8970 (p) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.2200 time to fit residues: 42.0739 Evaluate side-chains 98 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 88 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 9 optimal weight: 0.1980 chunk 42 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 25 optimal weight: 20.0000 chunk 78 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1069 ASN ** A1075 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1075 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1099 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8286 Z= 0.166 Angle : 0.553 8.671 11204 Z= 0.295 Chirality : 0.041 0.153 1200 Planarity : 0.005 0.042 1432 Dihedral : 5.724 42.822 1104 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.85 % 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: -0.57 (0.28), residues: 980 helix: 1.29 (0.24), residues: 450 sheet: -1.54 (0.48), residues: 122 loop : -1.96 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B1170 HIS 0.004 0.001 HIS B1012 PHE 0.019 0.001 PHE B 710 TYR 0.014 0.001 TYR A1043 ARG 0.005 0.000 ARG A1039 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 714 MET cc_start: 0.8454 (mpp) cc_final: 0.7855 (mpp) REVERT: A 856 TRP cc_start: 0.4232 (p-90) cc_final: 0.3615 (p-90) REVERT: A 882 LYS cc_start: 0.8525 (pttt) cc_final: 0.8154 (ptpp) REVERT: A 957 MET cc_start: 0.9487 (mmm) cc_final: 0.9069 (mmm) REVERT: A 1060 MET cc_start: 0.8028 (tmm) cc_final: 0.7543 (tmm) REVERT: A 1148 MET cc_start: 0.7020 (ptt) cc_final: 0.5783 (ptt) REVERT: A 1169 VAL cc_start: 0.9286 (t) cc_final: 0.8973 (p) REVERT: B 714 MET cc_start: 0.8446 (mpp) cc_final: 0.7881 (mpp) REVERT: B 905 ASN cc_start: 0.8593 (m110) cc_final: 0.8392 (m-40) REVERT: B 956 ARG cc_start: 0.8997 (mmt90) cc_final: 0.8751 (mmt90) REVERT: B 957 MET cc_start: 0.9472 (mmm) cc_final: 0.9056 (mmm) REVERT: B 966 TYR cc_start: 0.6548 (m-80) cc_final: 0.6292 (m-80) REVERT: B 1060 MET cc_start: 0.8102 (tmm) cc_final: 0.7460 (tmm) REVERT: B 1148 MET cc_start: 0.7164 (mtm) cc_final: 0.6954 (mtp) REVERT: B 1169 VAL cc_start: 0.9293 (t) cc_final: 0.9005 (p) outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.2185 time to fit residues: 41.7351 Evaluate side-chains 101 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 chunk 80 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 48 optimal weight: 8.9990 chunk 85 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1075 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1069 ASN ** B1075 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1099 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.3881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8286 Z= 0.182 Angle : 0.553 9.234 11204 Z= 0.296 Chirality : 0.041 0.168 1200 Planarity : 0.005 0.040 1432 Dihedral : 5.590 44.844 1104 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.75 % 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: -0.43 (0.28), residues: 980 helix: 1.45 (0.24), residues: 460 sheet: -1.47 (0.48), residues: 122 loop : -2.04 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A1170 HIS 0.004 0.001 HIS A1099 PHE 0.011 0.001 PHE B 710 TYR 0.023 0.002 TYR A 769 ARG 0.004 0.000 ARG B1039 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 714 MET cc_start: 0.8393 (mpp) cc_final: 0.7855 (mpp) REVERT: A 856 TRP cc_start: 0.3970 (p-90) cc_final: 0.3532 (p-90) REVERT: A 905 ASN cc_start: 0.8643 (m110) cc_final: 0.8236 (m110) REVERT: A 956 ARG cc_start: 0.9004 (mmt90) cc_final: 0.8758 (mmt90) REVERT: A 957 MET cc_start: 0.9496 (mmm) cc_final: 0.9092 (mmm) REVERT: A 1148 MET cc_start: 0.6943 (ptt) cc_final: 0.5707 (ptt) REVERT: A 1169 VAL cc_start: 0.9303 (t) cc_final: 0.8872 (t) REVERT: B 714 MET cc_start: 0.8430 (mpp) cc_final: 0.7938 (mpp) REVERT: B 856 TRP cc_start: 0.3488 (p-90) cc_final: 0.2620 (p-90) REVERT: B 905 ASN cc_start: 0.8610 (m110) cc_final: 0.8392 (m-40) REVERT: B 957 MET cc_start: 0.9484 (mmm) cc_final: 0.9069 (mmm) REVERT: B 966 TYR cc_start: 0.6553 (m-80) cc_final: 0.6272 (m-80) REVERT: B 1060 MET cc_start: 0.8115 (tmm) cc_final: 0.7428 (tmm) REVERT: B 1148 MET cc_start: 0.7266 (mtm) cc_final: 0.7059 (mtp) REVERT: B 1169 VAL cc_start: 0.9374 (t) cc_final: 0.8621 (t) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.2055 time to fit residues: 36.9778 Evaluate side-chains 96 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 0.8980 chunk 18 optimal weight: 8.9990 chunk 55 optimal weight: 1.9990 chunk 23 optimal weight: 30.0000 chunk 94 optimal weight: 1.9990 chunk 78 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 chunk 7 optimal weight: 7.9990 chunk 31 optimal weight: 20.0000 chunk 49 optimal weight: 20.0000 chunk 91 optimal weight: 4.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1075 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1075 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1099 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.4077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8286 Z= 0.208 Angle : 0.575 8.716 11204 Z= 0.308 Chirality : 0.042 0.192 1200 Planarity : 0.005 0.070 1432 Dihedral : 5.675 45.155 1104 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 17.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.85 % 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: -0.27 (0.28), residues: 980 helix: 1.64 (0.24), residues: 442 sheet: -1.54 (0.49), residues: 122 loop : -1.83 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 820 HIS 0.004 0.001 HIS B1099 PHE 0.010 0.001 PHE B 750 TYR 0.020 0.002 TYR B1124 ARG 0.008 0.001 ARG B1006 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 0.938 Fit side-chains revert: symmetry clash REVERT: A 714 MET cc_start: 0.8433 (mpp) cc_final: 0.7839 (mpp) REVERT: A 856 TRP cc_start: 0.3858 (p-90) cc_final: 0.3369 (p-90) REVERT: A 905 ASN cc_start: 0.8664 (m110) cc_final: 0.8270 (m110) REVERT: A 957 MET cc_start: 0.9499 (mmm) cc_final: 0.9097 (mmm) REVERT: A 966 TYR cc_start: 0.6333 (m-80) cc_final: 0.6131 (m-80) REVERT: A 1148 MET cc_start: 0.7038 (ptt) cc_final: 0.5756 (ptt) REVERT: A 1169 VAL cc_start: 0.9358 (t) cc_final: 0.8405 (t) REVERT: B 714 MET cc_start: 0.8447 (mpp) cc_final: 0.7981 (mpp) REVERT: B 833 GLU cc_start: 0.8272 (pt0) cc_final: 0.8041 (pt0) REVERT: B 856 TRP cc_start: 0.3599 (p-90) cc_final: 0.2738 (p-90) REVERT: B 905 ASN cc_start: 0.8668 (m110) cc_final: 0.8448 (m-40) REVERT: B 956 ARG cc_start: 0.9041 (mmt90) cc_final: 0.8838 (mmt90) REVERT: B 957 MET cc_start: 0.9483 (mmm) cc_final: 0.9057 (mmm) REVERT: B 966 TYR cc_start: 0.6486 (m-80) cc_final: 0.6216 (m-80) REVERT: B 1060 MET cc_start: 0.8117 (tmm) cc_final: 0.7580 (tmm) REVERT: B 1148 MET cc_start: 0.7317 (mtm) cc_final: 0.7078 (mtp) REVERT: B 1169 VAL cc_start: 0.9347 (t) cc_final: 0.8706 (t) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.1634 time to fit residues: 31.1174 Evaluate side-chains 100 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 0.8980 chunk 54 optimal weight: 6.9990 chunk 69 optimal weight: 7.9990 chunk 53 optimal weight: 0.8980 chunk 79 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 chunk 94 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 57 optimal weight: 20.0000 chunk 43 optimal weight: 0.8980 chunk 58 optimal weight: 7.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 774 HIS ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1075 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 774 HIS ** B 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1075 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1099 HIS ** B1186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.4244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8286 Z= 0.166 Angle : 0.564 9.060 11204 Z= 0.301 Chirality : 0.041 0.178 1200 Planarity : 0.005 0.051 1432 Dihedral : 5.468 45.036 1104 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.75 % 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: -0.08 (0.28), residues: 980 helix: 1.74 (0.24), residues: 452 sheet: -1.47 (0.50), residues: 122 loop : -1.71 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B1189 HIS 0.003 0.001 HIS B1099 PHE 0.009 0.001 PHE B 710 TYR 0.024 0.001 TYR A 769 ARG 0.006 0.000 ARG B1039 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 714 MET cc_start: 0.8411 (mpp) cc_final: 0.7795 (mpp) REVERT: A 848 TYR cc_start: 0.7406 (m-10) cc_final: 0.7204 (m-10) REVERT: A 856 TRP cc_start: 0.3817 (p-90) cc_final: 0.3328 (p-90) REVERT: A 905 ASN cc_start: 0.8695 (m110) cc_final: 0.8460 (m-40) REVERT: A 957 MET cc_start: 0.9476 (mmm) cc_final: 0.9052 (mmm) REVERT: A 966 TYR cc_start: 0.6333 (m-80) cc_final: 0.6133 (m-80) REVERT: A 1148 MET cc_start: 0.6976 (ptt) cc_final: 0.5878 (ptt) REVERT: B 714 MET cc_start: 0.8427 (mpp) cc_final: 0.7933 (mpp) REVERT: B 856 TRP cc_start: 0.3547 (p-90) cc_final: 0.2716 (p-90) REVERT: B 957 MET cc_start: 0.9475 (mmm) cc_final: 0.9010 (mmm) REVERT: B 966 TYR cc_start: 0.6518 (m-80) cc_final: 0.6237 (m-80) REVERT: B 1148 MET cc_start: 0.7284 (mtm) cc_final: 0.7038 (mtp) REVERT: B 1169 VAL cc_start: 0.9322 (t) cc_final: 0.8593 (t) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.1788 time to fit residues: 33.3539 Evaluate side-chains 96 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 0.9980 chunk 56 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 64 optimal weight: 8.9990 chunk 46 optimal weight: 0.1980 chunk 8 optimal weight: 6.9990 chunk 74 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1075 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 774 HIS ** B 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1075 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.4416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8286 Z= 0.168 Angle : 0.557 9.624 11204 Z= 0.297 Chirality : 0.041 0.187 1200 Planarity : 0.005 0.042 1432 Dihedral : 5.335 45.137 1104 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.53 % 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: 0.09 (0.28), residues: 980 helix: 1.90 (0.24), residues: 450 sheet: -1.33 (0.51), residues: 122 loop : -1.67 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B1189 HIS 0.003 0.001 HIS B1099 PHE 0.025 0.001 PHE B 710 TYR 0.017 0.001 TYR A1124 ARG 0.003 0.000 ARG B1039 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 714 MET cc_start: 0.8407 (mpp) cc_final: 0.7773 (mpp) REVERT: A 856 TRP cc_start: 0.3849 (p-90) cc_final: 0.3371 (p-90) REVERT: A 882 LYS cc_start: 0.8475 (pttt) cc_final: 0.8263 (ptpp) REVERT: A 905 ASN cc_start: 0.8719 (m110) cc_final: 0.8480 (m-40) REVERT: A 957 MET cc_start: 0.9474 (mmm) cc_final: 0.9057 (mmm) REVERT: A 966 TYR cc_start: 0.6330 (m-80) cc_final: 0.5991 (m-80) REVERT: A 1060 MET cc_start: 0.8177 (tmm) cc_final: 0.7873 (tmm) REVERT: A 1148 MET cc_start: 0.6943 (ptt) cc_final: 0.5724 (ptt) REVERT: B 714 MET cc_start: 0.8370 (mpp) cc_final: 0.7870 (mpp) REVERT: B 856 TRP cc_start: 0.3542 (p-90) cc_final: 0.2726 (p-90) REVERT: B 905 ASN cc_start: 0.8620 (m-40) cc_final: 0.8292 (m-40) REVERT: B 957 MET cc_start: 0.9475 (mmm) cc_final: 0.9004 (mmm) REVERT: B 1060 MET cc_start: 0.8066 (tmm) cc_final: 0.7551 (tmm) REVERT: B 1148 MET cc_start: 0.7286 (mtm) cc_final: 0.7078 (mtp) REVERT: B 1169 VAL cc_start: 0.9323 (t) cc_final: 0.8660 (t) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.1999 time to fit residues: 36.0240 Evaluate side-chains 96 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.7980 chunk 88 optimal weight: 10.0000 chunk 90 optimal weight: 3.9990 chunk 52 optimal weight: 7.9990 chunk 38 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 chunk 79 optimal weight: 10.0000 chunk 83 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 57 optimal weight: 20.0000 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1010 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1075 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 774 HIS ** B 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1075 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.4545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8286 Z= 0.182 Angle : 0.571 9.584 11204 Z= 0.301 Chirality : 0.042 0.179 1200 Planarity : 0.004 0.037 1432 Dihedral : 5.375 45.422 1104 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.53 % 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: 0.08 (0.28), residues: 980 helix: 1.87 (0.24), residues: 454 sheet: -1.17 (0.52), residues: 118 loop : -1.75 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B1170 HIS 0.004 0.001 HIS B 883 PHE 0.020 0.001 PHE B 710 TYR 0.028 0.002 TYR A 769 ARG 0.005 0.000 ARG B1039 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 714 MET cc_start: 0.8408 (mpp) cc_final: 0.7759 (mpp) REVERT: A 756 MET cc_start: 0.8204 (ptm) cc_final: 0.7743 (tpt) REVERT: A 856 TRP cc_start: 0.3814 (p-90) cc_final: 0.3383 (p-90) REVERT: A 905 ASN cc_start: 0.8724 (m110) cc_final: 0.8487 (m-40) REVERT: A 957 MET cc_start: 0.9472 (mmm) cc_final: 0.9043 (mmm) REVERT: A 966 TYR cc_start: 0.6303 (m-80) cc_final: 0.5948 (m-80) REVERT: A 1148 MET cc_start: 0.6977 (ptt) cc_final: 0.5736 (ptt) REVERT: B 714 MET cc_start: 0.8384 (mpp) cc_final: 0.7923 (mpp) REVERT: B 856 TRP cc_start: 0.3470 (p-90) cc_final: 0.2661 (p-90) REVERT: B 905 ASN cc_start: 0.8676 (m-40) cc_final: 0.8350 (m-40) REVERT: B 957 MET cc_start: 0.9479 (mmm) cc_final: 0.9019 (mmm) REVERT: B 966 TYR cc_start: 0.5604 (m-80) cc_final: 0.5326 (m-80) REVERT: B 1060 MET cc_start: 0.8095 (tmm) cc_final: 0.7846 (tmm) REVERT: B 1148 MET cc_start: 0.7331 (mtm) cc_final: 0.7108 (mtp) REVERT: B 1169 VAL cc_start: 0.9252 (t) cc_final: 0.8864 (t) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.1690 time to fit residues: 28.7460 Evaluate side-chains 91 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 93 optimal weight: 0.8980 chunk 56 optimal weight: 8.9990 chunk 44 optimal weight: 4.9990 chunk 64 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 77 optimal weight: 9.9990 chunk 8 optimal weight: 9.9990 chunk 60 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1010 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1075 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1075 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.4582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8286 Z= 0.199 Angle : 0.586 9.723 11204 Z= 0.309 Chirality : 0.042 0.181 1200 Planarity : 0.004 0.038 1432 Dihedral : 5.413 44.390 1104 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.64 % 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: 0.03 (0.28), residues: 980 helix: 1.86 (0.24), residues: 452 sheet: -1.15 (0.52), residues: 118 loop : -1.80 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 820 HIS 0.007 0.001 HIS A 883 PHE 0.020 0.001 PHE B 710 TYR 0.027 0.002 TYR B 769 ARG 0.006 0.000 ARG B1039 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 714 MET cc_start: 0.8412 (mpp) cc_final: 0.7786 (mpp) REVERT: A 756 MET cc_start: 0.8227 (ptm) cc_final: 0.7753 (tpt) REVERT: A 856 TRP cc_start: 0.3821 (p-90) cc_final: 0.3323 (p-90) REVERT: A 905 ASN cc_start: 0.8728 (m110) cc_final: 0.8487 (m-40) REVERT: A 957 MET cc_start: 0.9470 (mmm) cc_final: 0.9056 (mmm) REVERT: A 966 TYR cc_start: 0.6256 (m-80) cc_final: 0.5893 (m-80) REVERT: A 1060 MET cc_start: 0.8161 (tmm) cc_final: 0.7844 (tmm) REVERT: A 1148 MET cc_start: 0.6896 (ptt) cc_final: 0.5692 (ptt) REVERT: B 714 MET cc_start: 0.8407 (mpp) cc_final: 0.7909 (mpp) REVERT: B 856 TRP cc_start: 0.3507 (p-90) cc_final: 0.2600 (p-90) REVERT: B 905 ASN cc_start: 0.8682 (m-40) cc_final: 0.8361 (m-40) REVERT: B 957 MET cc_start: 0.9475 (mmm) cc_final: 0.9014 (mmm) REVERT: B 966 TYR cc_start: 0.5609 (m-80) cc_final: 0.5353 (m-80) REVERT: B 1060 MET cc_start: 0.8104 (tmm) cc_final: 0.7831 (tmm) REVERT: B 1148 MET cc_start: 0.7292 (mtm) cc_final: 0.6958 (ttm) REVERT: B 1169 VAL cc_start: 0.9330 (t) cc_final: 0.8754 (t) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.1709 time to fit residues: 28.5418 Evaluate side-chains 93 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.9990 chunk 23 optimal weight: 9.9990 chunk 71 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 77 optimal weight: 0.0770 chunk 32 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 chunk 9 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 overall best weight: 0.9944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1010 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1075 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1075 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.085228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.068221 restraints weight = 38943.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.070226 restraints weight = 25428.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.071740 restraints weight = 18620.765| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.4754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8286 Z= 0.151 Angle : 0.549 9.192 11204 Z= 0.288 Chirality : 0.041 0.169 1200 Planarity : 0.004 0.036 1432 Dihedral : 5.214 44.016 1104 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.64 % 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: 0.26 (0.29), residues: 980 helix: 2.01 (0.25), residues: 458 sheet: -1.01 (0.52), residues: 118 loop : -1.69 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B1189 HIS 0.004 0.001 HIS B1099 PHE 0.020 0.001 PHE B 710 TYR 0.023 0.001 TYR A 769 ARG 0.004 0.000 ARG B1039 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2048.31 seconds wall clock time: 37 minutes 58.94 seconds (2278.94 seconds total)