Starting phenix.real_space_refine (version: 1.21rc1) on Tue Jul 4 00:48:37 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ste_40759/07_2023/8ste_40759_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ste_40759/07_2023/8ste_40759.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ste_40759/07_2023/8ste_40759.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ste_40759/07_2023/8ste_40759.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ste_40759/07_2023/8ste_40759_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ste_40759/07_2023/8ste_40759_updated.pdb" } resolution = 3.34 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.063 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 S 38 5.16 5 Cl 2 4.86 5 C 3719 2.51 5 N 1020 2.21 5 O 1037 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 1119": "OE1" <-> "OE2" Residue "A GLU 1140": "OE1" <-> "OE2" Residue "B GLU 1106": "OE1" <-> "OE2" Residue "B GLU 1128": "OE1" <-> "OE2" Residue "B GLU 1188": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 5816 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2878 Classifications: {'peptide': 355} Link IDs: {'PTRANS': 13, 'TRANS': 341} Chain breaks: 1 Chain: "B" Number of atoms: 2896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2896 Classifications: {'peptide': 357} Link IDs: {'PTRANS': 13, 'TRANS': 343} Chain breaks: 1 Chain: "A" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'FUN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'FUN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.43, per 1000 atoms: 0.59 Number of scatterers: 5816 At special positions: 0 Unit cell: (78.11, 82.39, 113.42, 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) Cl 2 17.00 S 38 16.00 O 1037 8.00 N 1020 7.00 C 3719 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: 2.29 Conformation dependent library (CDL) restraints added in 868.0 milliseconds 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1352 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 4 sheets defined 43.1% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 764 through 779 Processing helix chain 'A' and resid 802 through 811 removed outlier: 3.797A pdb=" N PHE A 811 " --> pdb=" O LEU A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 848 Processing helix chain 'A' and resid 863 through 873 Processing helix chain 'A' and resid 897 through 912 Processing helix chain 'A' and resid 1035 through 1046 Proline residue: A1040 - end of helix removed outlier: 3.610A pdb=" N THR A1045 " --> pdb=" O TYR A1041 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LYS A1046 " --> pdb=" O LEU A1042 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1079 Processing helix chain 'A' and resid 1098 through 1111 Proline residue: A1110 - end of helix Processing helix chain 'A' and resid 1120 through 1129 Processing helix chain 'A' and resid 1136 through 1141 Processing helix chain 'A' and resid 1143 through 1159 Processing helix chain 'A' and resid 1180 through 1190 Processing helix chain 'B' and resid 764 through 779 Processing helix chain 'B' and resid 802 through 812 removed outlier: 3.817A pdb=" N PHE B 811 " --> pdb=" O LEU B 807 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR B 812 " --> pdb=" O VAL B 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 831 through 848 Processing helix chain 'B' and resid 863 through 873 Processing helix chain 'B' and resid 897 through 912 removed outlier: 3.560A pdb=" N PHE B 907 " --> pdb=" O TYR B 903 " (cutoff:3.500A) Processing helix chain 'B' and resid 1035 through 1044 Proline residue: B1040 - end of helix Processing helix chain 'B' and resid 1065 through 1079 Processing helix chain 'B' and resid 1098 through 1107 Processing helix chain 'B' and resid 1120 through 1129 Processing helix chain 'B' and resid 1136 through 1141 Processing helix chain 'B' and resid 1143 through 1159 Processing helix chain 'B' and resid 1180 through 1190 Processing sheet with id= A, first strand: chain 'A' and resid 1166 through 1169 removed outlier: 4.669A pdb=" N GLY A 887 " --> pdb=" O MET A 794 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 1023 through 1026 removed outlier: 6.264A pdb=" N LYS A1053 " --> pdb=" O ILE A1024 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N VAL A1026 " --> pdb=" O LYS A1053 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ARG A1055 " --> pdb=" O VAL A1026 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N ASP A1085 " --> pdb=" O VAL A1056 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ILE A1058 " --> pdb=" O ASP A1085 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N MET A1087 " --> pdb=" O ILE A1058 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 791 through 793 removed outlier: 6.791A pdb=" N THR B 883 " --> pdb=" O LEU B 792 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N GLY B 916 " --> pdb=" O LEU B 884 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N LEU B 886 " --> pdb=" O GLY B 916 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N VAL B 918 " --> pdb=" O LEU B 886 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE B1166 " --> pdb=" O LEU B1198 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N VAL B1200 " --> pdb=" O ILE B1166 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N MET B1168 " --> pdb=" O VAL B1200 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER B1169 " --> pdb=" O TRP B1027 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ASP B1085 " --> pdb=" O VAL B1056 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N ILE B1058 " --> pdb=" O ASP B1085 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N MET B1087 " --> pdb=" O ILE B1058 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 822 through 824 234 hydrogen bonds defined for protein. 699 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.64 Time building geometry restraints manager: 2.47 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: 1886 1.34 - 1.46: 1166 1.46 - 1.58: 2813 1.58 - 1.70: 0 1.70 - 1.82: 72 Bond restraints: 5937 Sorted by residual: bond pdb=" C4 FUN B1301 " pdb=" N2 FUN B1301 " ideal model delta sigma weight residual 1.340 1.462 -0.122 2.00e-02 2.50e+03 3.74e+01 bond pdb=" C4 FUN A1301 " pdb=" N2 FUN A1301 " ideal model delta sigma weight residual 1.340 1.450 -0.110 2.00e-02 2.50e+03 3.04e+01 bond pdb=" C7 FUN B1301 " pdb=" C8 FUN B1301 " ideal model delta sigma weight residual 1.429 1.359 0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" C7 FUN A1301 " pdb=" C8 FUN A1301 " ideal model delta sigma weight residual 1.429 1.359 0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" N1 FUN A1301 " pdb=" S1 FUN A1301 " ideal model delta sigma weight residual 1.647 1.707 -0.060 2.00e-02 2.50e+03 8.94e+00 ... (remaining 5932 not shown) Histogram of bond angle deviations from ideal: 99.84 - 106.67: 179 106.67 - 113.50: 3327 113.50 - 120.34: 2177 120.34 - 127.17: 2250 127.17 - 134.00: 79 Bond angle restraints: 8012 Sorted by residual: angle pdb=" O1 FUN B1301 " pdb=" S1 FUN B1301 " pdb=" O2 FUN B1301 " ideal model delta sigma weight residual 119.17 101.42 17.75 3.00e+00 1.11e-01 3.50e+01 angle pdb=" O1 FUN A1301 " pdb=" S1 FUN A1301 " pdb=" O2 FUN A1301 " ideal model delta sigma weight residual 119.17 101.65 17.52 3.00e+00 1.11e-01 3.41e+01 angle pdb=" C5 FUN B1301 " pdb=" C6 FUN B1301 " pdb=" O3 FUN B1301 " ideal model delta sigma weight residual 117.64 126.47 -8.83 3.00e+00 1.11e-01 8.67e+00 angle pdb=" C5 FUN A1301 " pdb=" C6 FUN A1301 " pdb=" O3 FUN A1301 " ideal model delta sigma weight residual 117.64 125.56 -7.92 3.00e+00 1.11e-01 6.97e+00 angle pdb=" N ILE B 913 " pdb=" CA ILE B 913 " pdb=" C ILE B 913 " ideal model delta sigma weight residual 111.91 109.70 2.21 8.90e-01 1.26e+00 6.18e+00 ... (remaining 8007 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 3233 17.61 - 35.23: 293 35.23 - 52.84: 56 52.84 - 70.46: 13 70.46 - 88.07: 6 Dihedral angle restraints: 3601 sinusoidal: 1519 harmonic: 2082 Sorted by residual: dihedral pdb=" CA PHE A1030 " pdb=" C PHE A1030 " pdb=" N ASP A1031 " pdb=" CA ASP A1031 " ideal model delta harmonic sigma weight residual -180.00 -154.80 -25.20 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA ASN A 849 " pdb=" C ASN A 849 " pdb=" N LYS A 850 " pdb=" CA LYS A 850 " ideal model delta harmonic sigma weight residual -180.00 -161.88 -18.12 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CG ARG B1055 " pdb=" CD ARG B1055 " pdb=" NE ARG B1055 " pdb=" CZ ARG B1055 " ideal model delta sinusoidal sigma weight residual -90.00 -133.56 43.56 2 1.50e+01 4.44e-03 1.01e+01 ... (remaining 3598 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 504 0.027 - 0.055: 241 0.055 - 0.082: 74 0.082 - 0.109: 45 0.109 - 0.136: 19 Chirality restraints: 883 Sorted by residual: chirality pdb=" CA ILE A1024 " pdb=" N ILE A1024 " pdb=" C ILE A1024 " pdb=" CB ILE A1024 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.65e-01 chirality pdb=" CA ILE B1165 " pdb=" N ILE B1165 " pdb=" C ILE B1165 " pdb=" CB ILE B1165 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.20e-01 chirality pdb=" CA ILE A1086 " pdb=" N ILE A1086 " pdb=" C ILE A1086 " pdb=" CB ILE A1086 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.95e-01 ... (remaining 880 not shown) Planarity restraints: 1009 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 880 " -0.024 5.00e-02 4.00e+02 3.55e-02 2.02e+00 pdb=" N PRO B 881 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 881 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 881 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B1195 " 0.018 5.00e-02 4.00e+02 2.79e-02 1.25e+00 pdb=" N PRO B1196 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO B1196 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO B1196 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO A1096 " 0.005 2.00e-02 2.50e+03 1.01e-02 1.02e+00 pdb=" C PRO A1096 " -0.017 2.00e-02 2.50e+03 pdb=" O PRO A1096 " 0.007 2.00e-02 2.50e+03 pdb=" N LYS A1097 " 0.006 2.00e-02 2.50e+03 ... (remaining 1006 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 48 2.56 - 3.15: 4941 3.15 - 3.73: 9024 3.73 - 4.32: 12173 4.32 - 4.90: 20893 Nonbonded interactions: 47079 Sorted by model distance: nonbonded pdb=" OD2 ASP B1025 " pdb=" OG SER B1160 " model vdw 1.979 2.440 nonbonded pdb=" O ASP B 810 " pdb=" NZ LYS B1046 " model vdw 2.055 2.520 nonbonded pdb=" OD1 ASP A 901 " pdb=" OG SER A1180 " model vdw 2.124 2.440 nonbonded pdb=" OD2 ASP A1025 " pdb=" OG SER A1160 " model vdw 2.145 2.440 nonbonded pdb=" ND2 ASN B1100 " pdb=" OE2 GLU B1154 " model vdw 2.146 2.520 ... (remaining 47074 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' and (resid 760 through 1208 or resid 1301)) } 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: 2.660 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: 13.770 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 19.320 Find NCS groups from input model: 0.390 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.122 5937 Z= 0.337 Angle : 0.695 17.754 8012 Z= 0.331 Chirality : 0.041 0.136 883 Planarity : 0.003 0.036 1009 Dihedral : 14.376 88.070 2249 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.32), residues: 704 helix: 1.48 (0.29), residues: 325 sheet: -1.30 (0.47), residues: 129 loop : -1.88 (0.35), residues: 250 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 0.724 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.2026 time to fit residues: 29.4688 Evaluate side-chains 85 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.740 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 40 optimal weight: 0.3980 chunk 63 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 868 GLN A1067 HIS A1164 ASN B 872 GLN ** B1100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1114 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 5937 Z= 0.216 Angle : 0.597 9.067 8012 Z= 0.283 Chirality : 0.045 0.185 883 Planarity : 0.004 0.040 1009 Dihedral : 8.006 89.854 780 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer Outliers : 1.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.32), residues: 704 helix: 1.57 (0.28), residues: 326 sheet: -1.34 (0.46), residues: 138 loop : -1.82 (0.35), residues: 240 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 97 time to evaluate : 0.725 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 103 average time/residue: 0.1997 time to fit residues: 26.6339 Evaluate side-chains 93 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 86 time to evaluate : 0.713 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0654 time to fit residues: 1.7673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 35 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 56 optimal weight: 7.9990 chunk 21 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 62 optimal weight: 9.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1164 ASN B 868 GLN ** B1100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.042 5937 Z= 0.311 Angle : 0.630 9.174 8012 Z= 0.299 Chirality : 0.045 0.175 883 Planarity : 0.004 0.044 1009 Dihedral : 7.932 87.545 780 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer Outliers : 1.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.31), residues: 704 helix: 1.42 (0.28), residues: 325 sheet: -1.23 (0.46), residues: 137 loop : -1.89 (0.36), residues: 242 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 96 time to evaluate : 0.687 Fit side-chains outliers start: 11 outliers final: 3 residues processed: 105 average time/residue: 0.2002 time to fit residues: 27.0704 Evaluate side-chains 88 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 85 time to evaluate : 0.701 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0576 time to fit residues: 1.3046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 47 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 56 optimal weight: 5.9990 chunk 38 optimal weight: 0.3980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1164 ASN ** B1100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 5937 Z= 0.237 Angle : 0.578 8.417 8012 Z= 0.277 Chirality : 0.043 0.127 883 Planarity : 0.004 0.045 1009 Dihedral : 7.715 86.273 780 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer Outliers : 1.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.31), residues: 704 helix: 1.43 (0.28), residues: 325 sheet: -1.19 (0.46), residues: 138 loop : -1.76 (0.36), residues: 241 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 96 time to evaluate : 0.666 Fit side-chains outliers start: 12 outliers final: 7 residues processed: 104 average time/residue: 0.2077 time to fit residues: 27.6763 Evaluate side-chains 93 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 86 time to evaluate : 0.705 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0644 time to fit residues: 1.7559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 5.9990 chunk 50 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 13 optimal weight: 0.0870 chunk 39 optimal weight: 0.2980 overall best weight: 0.6162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1164 ASN B 868 GLN ** B1100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1164 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 5937 Z= 0.203 Angle : 0.579 9.699 8012 Z= 0.277 Chirality : 0.042 0.136 883 Planarity : 0.004 0.045 1009 Dihedral : 7.521 85.070 780 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer Outliers : 0.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.32), residues: 704 helix: 1.53 (0.28), residues: 324 sheet: -0.96 (0.47), residues: 136 loop : -1.78 (0.36), residues: 244 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 97 time to evaluate : 0.716 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 101 average time/residue: 0.2061 time to fit residues: 26.8533 Evaluate side-chains 89 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 88 time to evaluate : 0.707 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0573 time to fit residues: 1.0729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 0.0770 chunk 67 optimal weight: 0.0980 chunk 56 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1114 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 5937 Z= 0.182 Angle : 0.559 7.851 8012 Z= 0.270 Chirality : 0.042 0.133 883 Planarity : 0.004 0.045 1009 Dihedral : 7.346 84.048 780 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer Outliers : 1.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.32), residues: 704 helix: 1.61 (0.28), residues: 323 sheet: -0.91 (0.47), residues: 138 loop : -1.72 (0.36), residues: 243 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 95 time to evaluate : 0.726 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 98 average time/residue: 0.2001 time to fit residues: 25.4337 Evaluate side-chains 93 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 88 time to evaluate : 0.711 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0690 time to fit residues: 1.5701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 38 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 26 optimal weight: 0.0870 chunk 40 optimal weight: 0.6980 chunk 20 optimal weight: 0.2980 chunk 13 optimal weight: 0.5980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1164 ASN ** B1100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1164 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 5937 Z= 0.183 Angle : 0.567 10.195 8012 Z= 0.270 Chirality : 0.042 0.180 883 Planarity : 0.004 0.048 1009 Dihedral : 7.212 83.002 780 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer Outliers : 0.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.32), residues: 704 helix: 1.60 (0.28), residues: 323 sheet: -0.78 (0.48), residues: 136 loop : -1.73 (0.36), residues: 245 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 93 time to evaluate : 0.718 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 97 average time/residue: 0.1922 time to fit residues: 24.4194 Evaluate side-chains 91 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 88 time to evaluate : 0.709 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0596 time to fit residues: 1.2814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 13 optimal weight: 0.2980 chunk 42 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 33 optimal weight: 0.0050 chunk 6 optimal weight: 3.9990 chunk 53 optimal weight: 0.5980 chunk 61 optimal weight: 7.9990 chunk 64 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1164 ASN ** B1100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 5937 Z= 0.192 Angle : 0.558 7.569 8012 Z= 0.270 Chirality : 0.042 0.177 883 Planarity : 0.004 0.065 1009 Dihedral : 7.097 82.291 780 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.32), residues: 704 helix: 1.64 (0.28), residues: 323 sheet: -0.75 (0.47), residues: 139 loop : -1.75 (0.36), residues: 242 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 92 time to evaluate : 0.705 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 93 average time/residue: 0.1906 time to fit residues: 23.0925 Evaluate side-chains 91 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 89 time to evaluate : 0.693 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0586 time to fit residues: 1.1794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 56 optimal weight: 0.0970 chunk 59 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1114 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 5937 Z= 0.199 Angle : 0.581 9.914 8012 Z= 0.277 Chirality : 0.042 0.162 883 Planarity : 0.004 0.079 1009 Dihedral : 7.070 81.779 780 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.32), residues: 704 helix: 1.60 (0.28), residues: 323 sheet: -0.67 (0.48), residues: 137 loop : -1.81 (0.35), residues: 244 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 91 time to evaluate : 0.743 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 92 average time/residue: 0.2018 time to fit residues: 24.1837 Evaluate side-chains 91 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 90 time to evaluate : 0.708 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0680 time to fit residues: 1.0927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 69 optimal weight: 0.0870 chunk 64 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 5 optimal weight: 0.0670 chunk 42 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 44 optimal weight: 0.3980 chunk 59 optimal weight: 0.0010 chunk 17 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 8 optimal weight: 0.0170 overall best weight: 0.1140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1164 ASN B1100 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 5937 Z= 0.136 Angle : 0.557 9.767 8012 Z= 0.270 Chirality : 0.041 0.169 883 Planarity : 0.004 0.074 1009 Dihedral : 6.844 83.213 780 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.32), residues: 704 helix: 1.74 (0.28), residues: 320 sheet: -0.58 (0.47), residues: 139 loop : -1.68 (0.35), residues: 245 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 102 time to evaluate : 0.709 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 103 average time/residue: 0.1997 time to fit residues: 26.5853 Evaluate side-chains 97 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 96 time to evaluate : 0.624 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0575 time to fit residues: 1.0419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 15 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 48 optimal weight: 0.0970 chunk 3 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1164 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.147367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.112675 restraints weight = 7230.186| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.68 r_work: 0.3180 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 5937 Z= 0.213 Angle : 0.589 10.110 8012 Z= 0.283 Chirality : 0.043 0.161 883 Planarity : 0.004 0.083 1009 Dihedral : 6.935 83.782 780 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.31), residues: 704 helix: 1.58 (0.28), residues: 323 sheet: -0.54 (0.47), residues: 137 loop : -1.81 (0.35), residues: 244 =============================================================================== Job complete usr+sys time: 1601.35 seconds wall clock time: 29 minutes 31.94 seconds (1771.94 seconds total)