Starting phenix.real_space_refine on Sun Mar 10 22:58:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ste_40759/03_2024/8ste_40759_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ste_40759/03_2024/8ste_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_40759/03_2024/8ste_40759.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ste_40759/03_2024/8ste_40759.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ste_40759/03_2024/8ste_40759_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ste_40759/03_2024/8ste_40759_updated.pdb" } resolution = 3.34 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= 0.063 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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 3.72, per 1000 atoms: 0.64 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: 2.30 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.16 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: 1.50 Time building geometry restraints manager: 2.50 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: 3.620 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: 13.660 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 20.170 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.030 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.690 ------------------------------------------------------------------------------- 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 % Allowed : 0.32 % Favored : 99.68 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1028 HIS 0.006 0.001 HIS B 908 PHE 0.013 0.002 PHE A 811 TYR 0.016 0.001 TYR A 903 ARG 0.006 0.001 ARG B 878 *********************** 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 : 0.730 Fit side-chains REVERT: A 863 LEU cc_start: 0.7996 (tp) cc_final: 0.7512 (mm) REVERT: A 868 GLN cc_start: 0.8707 (tp40) cc_final: 0.8474 (tp40) REVERT: A 903 TYR cc_start: 0.8747 (t80) cc_final: 0.8528 (t80) REVERT: B 912 ASP cc_start: 0.7657 (m-30) cc_final: 0.7302 (m-30) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.1947 time to fit residues: 28.4157 Evaluate side-chains 85 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.622 ------------------------------------------------------------------------------- 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: 0.8980 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: A1067 HIS A1164 ASN B 872 GLN ** B1100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1114 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5937 Z= 0.222 Angle : 0.606 9.137 8012 Z= 0.287 Chirality : 0.045 0.196 883 Planarity : 0.004 0.040 1009 Dihedral : 7.949 89.870 780 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 1.59 % Allowed : 8.60 % Favored : 89.81 % 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: -0.25 (0.32), residues: 704 helix: 1.55 (0.28), residues: 326 sheet: -1.33 (0.46), residues: 138 loop : -1.83 (0.35), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1028 HIS 0.004 0.001 HIS B 908 PHE 0.028 0.002 PHE A1030 TYR 0.015 0.001 TYR A 903 ARG 0.006 0.001 ARG B 878 *********************** 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 : 0.758 Fit side-chains revert: symmetry clash REVERT: A 914 GLN cc_start: 0.8213 (mt0) cc_final: 0.7981 (mt0) REVERT: A 1183 TYR cc_start: 0.8665 (t80) cc_final: 0.8334 (t80) REVERT: B 912 ASP cc_start: 0.7743 (m-30) cc_final: 0.7503 (m-30) REVERT: B 1047 LYS cc_start: 0.6975 (mttt) cc_final: 0.6714 (pttt) outliers start: 10 outliers final: 7 residues processed: 103 average time/residue: 0.2042 time to fit residues: 27.1547 Evaluate side-chains 94 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 87 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1032 ASP Chi-restraints excluded: chain A residue 1067 HIS Chi-restraints excluded: chain B residue 920 ILE Chi-restraints excluded: chain B residue 1091 ASP Chi-restraints excluded: chain B residue 1126 MET Chi-restraints excluded: chain B residue 1158 GLU Chi-restraints excluded: chain B residue 1165 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 35 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 62 optimal weight: 7.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1067 HIS A1164 ASN ** B1100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5937 Z= 0.273 Angle : 0.607 8.562 8012 Z= 0.289 Chirality : 0.044 0.151 883 Planarity : 0.004 0.044 1009 Dihedral : 7.984 88.661 780 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 2.39 % Allowed : 10.03 % Favored : 87.58 % 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 (0.31), residues: 704 helix: 1.43 (0.28), residues: 325 sheet: -1.21 (0.46), residues: 136 loop : -1.86 (0.35), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1028 HIS 0.007 0.001 HIS A1067 PHE 0.022 0.002 PHE A1030 TYR 0.015 0.001 TYR A 903 ARG 0.008 0.001 ARG A 898 *********************** 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 105 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 90 time to evaluate : 0.720 Fit side-chains REVERT: A 863 LEU cc_start: 0.7925 (tp) cc_final: 0.7404 (mm) REVERT: A 870 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8464 (mt) REVERT: A 914 GLN cc_start: 0.8218 (mt0) cc_final: 0.7990 (mt0) REVERT: B 912 ASP cc_start: 0.7738 (m-30) cc_final: 0.7499 (m-30) REVERT: B 1047 LYS cc_start: 0.7012 (mttt) cc_final: 0.6738 (pttt) outliers start: 15 outliers final: 9 residues processed: 100 average time/residue: 0.1939 time to fit residues: 25.1625 Evaluate side-chains 97 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 87 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 1032 ASP Chi-restraints excluded: chain A residue 1067 HIS Chi-restraints excluded: chain B residue 771 LEU Chi-restraints excluded: chain B residue 920 ILE Chi-restraints excluded: chain B residue 1091 ASP Chi-restraints excluded: chain B residue 1126 MET Chi-restraints excluded: chain B residue 1158 GLU Chi-restraints excluded: chain B residue 1165 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 47 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 56 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1067 HIS A1164 ASN ** B1100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5937 Z= 0.242 Angle : 0.579 8.169 8012 Z= 0.278 Chirality : 0.043 0.132 883 Planarity : 0.004 0.044 1009 Dihedral : 7.894 87.846 780 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 2.87 % Allowed : 11.78 % Favored : 85.35 % 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: -0.27 (0.31), residues: 704 helix: 1.41 (0.28), residues: 325 sheet: -1.14 (0.46), residues: 138 loop : -1.78 (0.36), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1028 HIS 0.005 0.001 HIS B 908 PHE 0.020 0.001 PHE A1030 TYR 0.014 0.001 TYR A 903 ARG 0.006 0.000 ARG B 878 *********************** 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 111 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 93 time to evaluate : 0.648 Fit side-chains REVERT: A 863 LEU cc_start: 0.7928 (tp) cc_final: 0.7406 (mm) REVERT: A 870 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8448 (mt) REVERT: A 914 GLN cc_start: 0.8205 (mt0) cc_final: 0.7965 (mt0) REVERT: B 912 ASP cc_start: 0.7722 (m-30) cc_final: 0.7493 (m-30) REVERT: B 1047 LYS cc_start: 0.7006 (mttt) cc_final: 0.6654 (pttt) REVERT: B 1072 MET cc_start: 0.6597 (mmm) cc_final: 0.6345 (ttt) outliers start: 18 outliers final: 12 residues processed: 106 average time/residue: 0.1890 time to fit residues: 25.9703 Evaluate side-chains 99 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 86 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 1032 ASP Chi-restraints excluded: chain A residue 1067 HIS Chi-restraints excluded: chain B residue 771 LEU Chi-restraints excluded: chain B residue 920 ILE Chi-restraints excluded: chain B residue 1089 LEU Chi-restraints excluded: chain B residue 1091 ASP Chi-restraints excluded: chain B residue 1114 HIS Chi-restraints excluded: chain B residue 1126 MET Chi-restraints excluded: chain B residue 1158 GLU Chi-restraints excluded: chain B residue 1165 ILE 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: 0.8980 chunk 27 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 60 optimal weight: 0.0370 chunk 17 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 13 optimal weight: 0.3980 chunk 39 optimal weight: 0.8980 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1067 HIS A1164 ASN ** B1100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.1751 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= 0.196 Angle : 0.569 9.198 8012 Z= 0.274 Chirality : 0.042 0.131 883 Planarity : 0.004 0.043 1009 Dihedral : 7.715 85.749 780 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.23 % Allowed : 13.06 % Favored : 84.71 % 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: -0.17 (0.31), residues: 704 helix: 1.51 (0.28), residues: 323 sheet: -0.99 (0.47), residues: 136 loop : -1.79 (0.35), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1028 HIS 0.004 0.001 HIS B 908 PHE 0.019 0.001 PHE A1030 TYR 0.014 0.001 TYR A 903 ARG 0.010 0.001 ARG A 898 *********************** 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 110 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 96 time to evaluate : 0.703 Fit side-chains REVERT: A 870 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8373 (mt) REVERT: A 914 GLN cc_start: 0.8200 (mt0) cc_final: 0.7940 (mt0) REVERT: A 1120 GLN cc_start: 0.7632 (mm-40) cc_final: 0.7376 (mm-40) REVERT: A 1161 SER cc_start: 0.8767 (t) cc_final: 0.8462 (p) REVERT: A 1183 TYR cc_start: 0.8707 (t80) cc_final: 0.8308 (t80) REVERT: B 844 ARG cc_start: 0.7442 (ttp80) cc_final: 0.7168 (ttp-110) REVERT: B 1047 LYS cc_start: 0.6987 (mttt) cc_final: 0.6644 (pttt) outliers start: 14 outliers final: 12 residues processed: 105 average time/residue: 0.1951 time to fit residues: 26.5061 Evaluate side-chains 100 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 87 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 849 ASN Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 1032 ASP Chi-restraints excluded: chain A residue 1067 HIS Chi-restraints excluded: chain B residue 771 LEU Chi-restraints excluded: chain B residue 920 ILE Chi-restraints excluded: chain B residue 1089 LEU Chi-restraints excluded: chain B residue 1091 ASP Chi-restraints excluded: chain B residue 1114 HIS Chi-restraints excluded: chain B residue 1126 MET Chi-restraints excluded: chain B residue 1158 GLU Chi-restraints excluded: chain B residue 1165 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 2.9990 chunk 67 optimal weight: 0.0000 chunk 56 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 5 optimal weight: 0.3980 chunk 22 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1067 HIS ** 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: 0.7729 moved from start: 0.1949 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= 0.207 Angle : 0.557 7.457 8012 Z= 0.272 Chirality : 0.042 0.128 883 Planarity : 0.004 0.044 1009 Dihedral : 7.573 84.307 780 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.71 % Allowed : 13.54 % Favored : 83.76 % 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: -0.12 (0.32), residues: 704 helix: 1.53 (0.28), residues: 322 sheet: -0.96 (0.47), residues: 138 loop : -1.73 (0.36), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1028 HIS 0.003 0.001 HIS B 908 PHE 0.018 0.001 PHE A1030 TYR 0.014 0.001 TYR A 903 ARG 0.007 0.000 ARG A 898 *********************** 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 109 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 92 time to evaluate : 0.710 Fit side-chains REVERT: A 870 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8371 (mt) REVERT: A 914 GLN cc_start: 0.8212 (mt0) cc_final: 0.7980 (mt0) REVERT: A 1067 HIS cc_start: 0.7858 (OUTLIER) cc_final: 0.7251 (p-80) REVERT: A 1120 GLN cc_start: 0.7574 (mm-40) cc_final: 0.7358 (mm-40) REVERT: A 1161 SER cc_start: 0.8747 (t) cc_final: 0.8471 (p) REVERT: A 1183 TYR cc_start: 0.8707 (t80) cc_final: 0.8290 (t80) REVERT: B 844 ARG cc_start: 0.7447 (ttp80) cc_final: 0.7169 (ttp-110) REVERT: B 1047 LYS cc_start: 0.6989 (mttt) cc_final: 0.6652 (pttt) outliers start: 17 outliers final: 9 residues processed: 104 average time/residue: 0.1974 time to fit residues: 26.7486 Evaluate side-chains 100 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 89 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 849 ASN Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 1032 ASP Chi-restraints excluded: chain A residue 1067 HIS Chi-restraints excluded: chain B residue 771 LEU Chi-restraints excluded: chain B residue 920 ILE Chi-restraints excluded: chain B residue 1091 ASP Chi-restraints excluded: chain B residue 1114 HIS Chi-restraints excluded: chain B residue 1126 MET Chi-restraints excluded: chain B residue 1158 GLU Chi-restraints excluded: chain B residue 1165 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 38 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 67 optimal weight: 0.0980 chunk 42 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 26 optimal weight: 0.0870 chunk 40 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1067 HIS A1164 ASN ** 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: 0.7717 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5937 Z= 0.185 Angle : 0.568 9.404 8012 Z= 0.274 Chirality : 0.042 0.134 883 Planarity : 0.004 0.049 1009 Dihedral : 7.439 83.587 780 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.55 % Allowed : 14.81 % Favored : 82.64 % 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: -0.05 (0.32), residues: 704 helix: 1.55 (0.28), residues: 322 sheet: -0.83 (0.47), residues: 138 loop : -1.71 (0.36), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1028 HIS 0.004 0.001 HIS B 908 PHE 0.018 0.001 PHE A1030 TYR 0.014 0.001 TYR A 903 ARG 0.011 0.000 ARG A 898 *********************** 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 110 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 94 time to evaluate : 0.709 Fit side-chains REVERT: A 870 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8335 (mt) REVERT: A 914 GLN cc_start: 0.8208 (mt0) cc_final: 0.7967 (mt0) REVERT: A 1161 SER cc_start: 0.8738 (t) cc_final: 0.8473 (p) REVERT: A 1183 TYR cc_start: 0.8698 (t80) cc_final: 0.8280 (t80) REVERT: B 844 ARG cc_start: 0.7428 (ttp80) cc_final: 0.7167 (ttp-110) REVERT: B 1047 LYS cc_start: 0.6979 (mttt) cc_final: 0.6644 (pttt) outliers start: 16 outliers final: 11 residues processed: 105 average time/residue: 0.1933 time to fit residues: 26.3338 Evaluate side-chains 99 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 87 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 849 ASN Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 1032 ASP Chi-restraints excluded: chain A residue 1067 HIS Chi-restraints excluded: chain A residue 1076 LEU Chi-restraints excluded: chain B residue 771 LEU Chi-restraints excluded: chain B residue 920 ILE Chi-restraints excluded: chain B residue 1091 ASP Chi-restraints excluded: chain B residue 1114 HIS Chi-restraints excluded: chain B residue 1126 MET Chi-restraints excluded: chain B residue 1158 GLU Chi-restraints excluded: chain B residue 1165 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 13 optimal weight: 0.0870 chunk 42 optimal weight: 4.9990 chunk 45 optimal weight: 0.0010 chunk 33 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 61 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.6966 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1067 HIS A1164 ASN ** B1100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5937 Z= 0.221 Angle : 0.572 7.583 8012 Z= 0.278 Chirality : 0.043 0.170 883 Planarity : 0.004 0.052 1009 Dihedral : 7.360 82.818 780 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.23 % Allowed : 15.45 % Favored : 82.32 % 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: -0.07 (0.32), residues: 704 helix: 1.53 (0.28), residues: 321 sheet: -0.78 (0.47), residues: 138 loop : -1.72 (0.36), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1028 HIS 0.004 0.001 HIS A1067 PHE 0.017 0.001 PHE A1030 TYR 0.013 0.001 TYR A 903 ARG 0.013 0.001 ARG A 898 *********************** 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 100 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 86 time to evaluate : 0.646 Fit side-chains REVERT: A 870 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8371 (mt) REVERT: A 914 GLN cc_start: 0.8226 (mt0) cc_final: 0.7987 (mt0) REVERT: A 1067 HIS cc_start: 0.7927 (OUTLIER) cc_final: 0.7539 (p-80) REVERT: A 1161 SER cc_start: 0.8758 (t) cc_final: 0.8477 (p) REVERT: A 1183 TYR cc_start: 0.8697 (t80) cc_final: 0.8338 (t80) REVERT: B 844 ARG cc_start: 0.7474 (ttp80) cc_final: 0.7195 (ttp-110) REVERT: B 1047 LYS cc_start: 0.6981 (mttt) cc_final: 0.6647 (pttt) outliers start: 14 outliers final: 10 residues processed: 96 average time/residue: 0.1837 time to fit residues: 22.9669 Evaluate side-chains 99 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 87 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 849 ASN Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 1032 ASP Chi-restraints excluded: chain A residue 1067 HIS Chi-restraints excluded: chain A residue 1076 LEU Chi-restraints excluded: chain B residue 771 LEU Chi-restraints excluded: chain B residue 920 ILE Chi-restraints excluded: chain B residue 1089 LEU Chi-restraints excluded: chain B residue 1091 ASP Chi-restraints excluded: chain B residue 1114 HIS Chi-restraints excluded: chain B residue 1126 MET Chi-restraints excluded: chain B residue 1165 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 19 optimal weight: 0.0170 chunk 56 optimal weight: 1.9990 chunk 59 optimal weight: 0.0370 chunk 62 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 overall best weight: 0.3696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1067 HIS ** B1100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5937 Z= 0.168 Angle : 0.568 9.345 8012 Z= 0.274 Chirality : 0.042 0.176 883 Planarity : 0.004 0.072 1009 Dihedral : 7.204 82.858 780 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.91 % Allowed : 16.72 % Favored : 81.37 % 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: 1.56 (0.28), residues: 321 sheet: -0.73 (0.47), residues: 138 loop : -1.72 (0.36), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1028 HIS 0.006 0.001 HIS A1067 PHE 0.017 0.001 PHE A1030 TYR 0.013 0.001 TYR A 903 ARG 0.016 0.001 ARG A 898 *********************** 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 104 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 92 time to evaluate : 0.696 Fit side-chains REVERT: A 870 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8322 (mt) REVERT: A 914 GLN cc_start: 0.8221 (mt0) cc_final: 0.7999 (mt0) REVERT: A 1161 SER cc_start: 0.8733 (t) cc_final: 0.8464 (p) REVERT: A 1183 TYR cc_start: 0.8683 (t80) cc_final: 0.8413 (t80) REVERT: B 844 ARG cc_start: 0.7423 (ttp80) cc_final: 0.7157 (ttp-110) REVERT: B 1047 LYS cc_start: 0.6956 (mttt) cc_final: 0.6624 (pttt) outliers start: 12 outliers final: 11 residues processed: 100 average time/residue: 0.1837 time to fit residues: 24.0801 Evaluate side-chains 101 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 89 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 849 ASN Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 1032 ASP Chi-restraints excluded: chain A residue 1067 HIS Chi-restraints excluded: chain A residue 1076 LEU Chi-restraints excluded: chain B residue 771 LEU Chi-restraints excluded: chain B residue 920 ILE Chi-restraints excluded: chain B residue 1089 LEU Chi-restraints excluded: chain B residue 1091 ASP Chi-restraints excluded: chain B residue 1114 HIS Chi-restraints excluded: chain B residue 1126 MET Chi-restraints excluded: chain B residue 1165 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 69 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 5 optimal weight: 0.0980 chunk 42 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 44 optimal weight: 0.0670 chunk 59 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1067 HIS A1164 ASN ** B1100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5937 Z= 0.179 Angle : 0.567 8.035 8012 Z= 0.274 Chirality : 0.042 0.178 883 Planarity : 0.004 0.079 1009 Dihedral : 7.072 82.524 780 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.07 % Allowed : 16.24 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.31), residues: 704 helix: 1.59 (0.28), residues: 321 sheet: -0.76 (0.47), residues: 139 loop : -1.78 (0.35), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1028 HIS 0.006 0.001 HIS A1067 PHE 0.017 0.001 PHE A1030 TYR 0.013 0.001 TYR A 903 ARG 0.020 0.001 ARG A 898 ********************** 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 103 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 90 time to evaluate : 0.699 Fit side-chains REVERT: A 870 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8327 (mt) REVERT: A 1161 SER cc_start: 0.8669 (t) cc_final: 0.8409 (p) REVERT: A 1183 TYR cc_start: 0.8681 (t80) cc_final: 0.8412 (t80) REVERT: B 844 ARG cc_start: 0.7428 (ttp80) cc_final: 0.7162 (ttp-110) REVERT: B 1047 LYS cc_start: 0.6956 (mttt) cc_final: 0.6627 (pttt) outliers start: 13 outliers final: 10 residues processed: 98 average time/residue: 0.1862 time to fit residues: 23.8973 Evaluate side-chains 101 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 90 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 849 ASN Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 1032 ASP Chi-restraints excluded: chain A residue 1067 HIS Chi-restraints excluded: chain B residue 771 LEU Chi-restraints excluded: chain B residue 920 ILE Chi-restraints excluded: chain B residue 1089 LEU Chi-restraints excluded: chain B residue 1091 ASP Chi-restraints excluded: chain B residue 1114 HIS Chi-restraints excluded: chain B residue 1126 MET Chi-restraints excluded: chain B residue 1165 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 15 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 48 optimal weight: 0.0570 chunk 3 optimal weight: 0.7980 chunk 40 optimal weight: 0.2980 chunk 63 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1067 HIS A1164 ASN ** B1100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.146971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.112223 restraints weight = 7237.698| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.68 r_work: 0.3162 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2357 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= 0.192 Angle : 0.586 9.641 8012 Z= 0.280 Chirality : 0.042 0.174 883 Planarity : 0.005 0.082 1009 Dihedral : 7.000 82.202 780 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.07 % Allowed : 16.56 % Favored : 81.37 % 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: -0.10 (0.31), residues: 704 helix: 1.52 (0.28), residues: 321 sheet: -0.76 (0.46), residues: 139 loop : -1.79 (0.35), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 892 HIS 0.005 0.001 HIS A1067 PHE 0.016 0.001 PHE A1030 TYR 0.013 0.001 TYR A 903 ARG 0.019 0.001 ARG A 898 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1728.02 seconds wall clock time: 31 minutes 59.86 seconds (1919.86 seconds total)