Starting phenix.real_space_refine on Fri Apr 5 18:16:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oo9_17007/04_2024/8oo9_17007_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oo9_17007/04_2024/8oo9_17007.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oo9_17007/04_2024/8oo9_17007.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oo9_17007/04_2024/8oo9_17007.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oo9_17007/04_2024/8oo9_17007_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oo9_17007/04_2024/8oo9_17007_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.014 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: 8 Type Number sf(0) Gaussians Al 1 5.89 5 P 44 5.49 5 Mg 1 5.21 5 S 24 5.16 5 C 2737 2.51 5 N 802 2.21 5 O 903 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G PHE 1615": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 4516 Number of models: 1 Model: "" Number of chains: 4 Chain: "G" Number of atoms: 3622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3622 Classifications: {'peptide': 439} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 425} Chain breaks: 3 Chain: "K" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 431 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "L" Number of atoms: 430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 430 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'ALF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 3.30, per 1000 atoms: 0.73 Number of scatterers: 4516 At special positions: 0 Unit cell: (78.09, 78.912, 83.022, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 24 16.00 P 44 15.00 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 903 8.00 N 802 7.00 C 2737 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.50 Conformation dependent library (CDL) restraints added in 677.1 milliseconds 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 836 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 20 helices and 2 sheets defined 46.2% alpha, 10.3% beta 14 base pairs and 38 stacking pairs defined. Time for finding SS restraints: 2.25 Creating SS restraints... Processing helix chain 'G' and resid 974 through 988 Processing helix chain 'G' and resid 1003 through 1018 Processing helix chain 'G' and resid 1030 through 1043 removed outlier: 4.701A pdb=" N HIS G1034 " --> pdb=" O ALA G1030 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ASN G1035 " --> pdb=" O SER G1031 " (cutoff:3.500A) Processing helix chain 'G' and resid 1056 through 1065 removed outlier: 4.273A pdb=" N LYS G1064 " --> pdb=" O LYS G1060 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N PHE G1065 " --> pdb=" O VAL G1061 " (cutoff:3.500A) Processing helix chain 'G' and resid 1088 through 1091 No H-bonds generated for 'chain 'G' and resid 1088 through 1091' Processing helix chain 'G' and resid 1093 through 1098 removed outlier: 4.309A pdb=" N LYS G1098 " --> pdb=" O ALA G1094 " (cutoff:3.500A) Processing helix chain 'G' and resid 1109 through 1111 No H-bonds generated for 'chain 'G' and resid 1109 through 1111' Processing helix chain 'G' and resid 1118 through 1124 Processing helix chain 'G' and resid 1143 through 1153 removed outlier: 3.658A pdb=" N LEU G1149 " --> pdb=" O GLU G1145 " (cutoff:3.500A) Processing helix chain 'G' and resid 1187 through 1193 removed outlier: 3.707A pdb=" N MET G1192 " --> pdb=" O LYS G1188 " (cutoff:3.500A) Processing helix chain 'G' and resid 1203 through 1206 No H-bonds generated for 'chain 'G' and resid 1203 through 1206' Processing helix chain 'G' and resid 1224 through 1238 removed outlier: 4.293A pdb=" N GLN G1236 " --> pdb=" O SER G1232 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ILE G1237 " --> pdb=" O LEU G1233 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N SER G1238 " --> pdb=" O ARG G1234 " (cutoff:3.500A) Processing helix chain 'G' and resid 1257 through 1269 removed outlier: 3.740A pdb=" N MET G1262 " --> pdb=" O MET G1258 " (cutoff:3.500A) Processing helix chain 'G' and resid 1271 through 1274 No H-bonds generated for 'chain 'G' and resid 1271 through 1274' Processing helix chain 'G' and resid 1545 through 1550 Processing helix chain 'G' and resid 1553 through 1567 removed outlier: 3.730A pdb=" N GLU G1567 " --> pdb=" O ARG G1563 " (cutoff:3.500A) Processing helix chain 'G' and resid 1579 through 1591 removed outlier: 3.563A pdb=" N GLU G1586 " --> pdb=" O ILE G1582 " (cutoff:3.500A) Processing helix chain 'G' and resid 1605 through 1617 Processing helix chain 'G' and resid 1652 through 1659 Processing helix chain 'G' and resid 1682 through 1700 removed outlier: 3.513A pdb=" N LYS G1693 " --> pdb=" O ARG G1689 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU G1694 " --> pdb=" O ALA G1690 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU G1695 " --> pdb=" O LEU G1691 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'G' and resid 993 through 995 removed outlier: 4.028A pdb=" N GLY G 993 " --> pdb=" O ARG G1131 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU G1133 " --> pdb=" O GLY G 993 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N MET G1104 " --> pdb=" O LEU G1132 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N LEU G1134 " --> pdb=" O MET G1104 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU G1106 " --> pdb=" O LEU G1134 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N SER G1085 " --> pdb=" O TYR G1052 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'G' and resid 1214 through 1220 removed outlier: 3.679A pdb=" N PHE G1576 " --> pdb=" O LEU G1626 " (cutoff:3.500A) 139 hydrogen bonds defined for protein. 417 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 34 hydrogen bonds 68 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 38 stacking parallelities Total time for adding SS restraints: 1.80 Time building geometry restraints manager: 2.29 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: 1330 1.34 - 1.46: 1151 1.46 - 1.58: 2088 1.58 - 1.70: 78 1.70 - 1.82: 46 Bond restraints: 4693 Sorted by residual: bond pdb=" F1 ALF G2003 " pdb="AL ALF G2003 " ideal model delta sigma weight residual 1.684 1.799 -0.115 2.00e-02 2.50e+03 3.33e+01 bond pdb=" F3 ALF G2003 " pdb="AL ALF G2003 " ideal model delta sigma weight residual 1.685 1.795 -0.110 2.00e-02 2.50e+03 3.03e+01 bond pdb=" F4 ALF G2003 " pdb="AL ALF G2003 " ideal model delta sigma weight residual 1.686 1.778 -0.092 2.00e-02 2.50e+03 2.09e+01 bond pdb=" F2 ALF G2003 " pdb="AL ALF G2003 " ideal model delta sigma weight residual 1.685 1.775 -0.090 2.00e-02 2.50e+03 2.02e+01 bond pdb=" C4' DG L -36 " pdb=" C3' DG L -36 " ideal model delta sigma weight residual 1.523 1.587 -0.064 2.00e-02 2.50e+03 1.04e+01 ... (remaining 4688 not shown) Histogram of bond angle deviations from ideal: 88.48 - 106.72: 444 106.72 - 124.96: 5843 124.96 - 143.21: 223 143.21 - 161.45: 0 161.45 - 179.69: 2 Bond angle restraints: 6512 Sorted by residual: angle pdb=" F3 ALF G2003 " pdb="AL ALF G2003 " pdb=" F4 ALF G2003 " ideal model delta sigma weight residual 109.63 179.69 -70.06 3.00e+00 1.11e-01 5.45e+02 angle pdb=" F1 ALF G2003 " pdb="AL ALF G2003 " pdb=" F2 ALF G2003 " ideal model delta sigma weight residual 108.68 178.52 -69.84 3.00e+00 1.11e-01 5.42e+02 angle pdb=" F1 ALF G2003 " pdb="AL ALF G2003 " pdb=" F4 ALF G2003 " ideal model delta sigma weight residual 109.02 88.48 20.54 3.00e+00 1.11e-01 4.69e+01 angle pdb=" F2 ALF G2003 " pdb="AL ALF G2003 " pdb=" F4 ALF G2003 " ideal model delta sigma weight residual 110.21 90.04 20.17 3.00e+00 1.11e-01 4.52e+01 angle pdb=" F2 ALF G2003 " pdb="AL ALF G2003 " pdb=" F3 ALF G2003 " ideal model delta sigma weight residual 109.59 89.92 19.67 3.00e+00 1.11e-01 4.30e+01 ... (remaining 6507 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.81: 2477 32.81 - 65.62: 214 65.62 - 98.43: 7 98.43 - 131.25: 2 131.25 - 164.06: 1 Dihedral angle restraints: 2701 sinusoidal: 1412 harmonic: 1289 Sorted by residual: dihedral pdb=" O1B ADP G2001 " pdb=" O3A ADP G2001 " pdb=" PB ADP G2001 " pdb=" PA ADP G2001 " ideal model delta sinusoidal sigma weight residual 300.00 135.94 164.06 1 2.00e+01 2.50e-03 4.71e+01 dihedral pdb=" C5' ADP G2001 " pdb=" O5' ADP G2001 " pdb=" PA ADP G2001 " pdb=" O2A ADP G2001 " ideal model delta sinusoidal sigma weight residual 300.00 169.04 130.97 1 2.00e+01 2.50e-03 3.97e+01 dihedral pdb=" O2A ADP G2001 " pdb=" O3A ADP G2001 " pdb=" PA ADP G2001 " pdb=" PB ADP G2001 " ideal model delta sinusoidal sigma weight residual -60.00 53.46 -113.46 1 2.00e+01 2.50e-03 3.36e+01 ... (remaining 2698 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 442 0.054 - 0.107: 219 0.107 - 0.160: 49 0.160 - 0.214: 8 0.214 - 0.267: 2 Chirality restraints: 720 Sorted by residual: chirality pdb=" CB ILE G1582 " pdb=" CA ILE G1582 " pdb=" CG1 ILE G1582 " pdb=" CG2 ILE G1582 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" C2' ADP G2001 " pdb=" C1' ADP G2001 " pdb=" C3' ADP G2001 " pdb=" O2' ADP G2001 " both_signs ideal model delta sigma weight residual False -2.51 -2.73 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CB ILE G1701 " pdb=" CA ILE G1701 " pdb=" CG1 ILE G1701 " pdb=" CG2 ILE G1701 " both_signs ideal model delta sigma weight residual False 2.64 2.85 -0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 717 not shown) Planarity restraints: 667 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC K 33 " -0.071 2.00e-02 2.50e+03 3.63e-02 2.97e+01 pdb=" N1 DC K 33 " 0.077 2.00e-02 2.50e+03 pdb=" C2 DC K 33 " 0.011 2.00e-02 2.50e+03 pdb=" O2 DC K 33 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DC K 33 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DC K 33 " -0.009 2.00e-02 2.50e+03 pdb=" N4 DC K 33 " -0.020 2.00e-02 2.50e+03 pdb=" C5 DC K 33 " -0.004 2.00e-02 2.50e+03 pdb=" C6 DC K 33 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC L -25 " 0.059 2.00e-02 2.50e+03 3.28e-02 2.43e+01 pdb=" N1 DC L -25 " -0.075 2.00e-02 2.50e+03 pdb=" C2 DC L -25 " -0.015 2.00e-02 2.50e+03 pdb=" O2 DC L -25 " 0.000 2.00e-02 2.50e+03 pdb=" N3 DC L -25 " 0.010 2.00e-02 2.50e+03 pdb=" C4 DC L -25 " 0.008 2.00e-02 2.50e+03 pdb=" N4 DC L -25 " 0.013 2.00e-02 2.50e+03 pdb=" C5 DC L -25 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DC L -25 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC L -28 " 0.048 2.00e-02 2.50e+03 2.77e-02 1.73e+01 pdb=" N1 DC L -28 " -0.066 2.00e-02 2.50e+03 pdb=" C2 DC L -28 " -0.011 2.00e-02 2.50e+03 pdb=" O2 DC L -28 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DC L -28 " 0.008 2.00e-02 2.50e+03 pdb=" C4 DC L -28 " 0.006 2.00e-02 2.50e+03 pdb=" N4 DC L -28 " 0.010 2.00e-02 2.50e+03 pdb=" C5 DC L -28 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DC L -28 " 0.002 2.00e-02 2.50e+03 ... (remaining 664 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 13 2.48 - 3.09: 3124 3.09 - 3.69: 7060 3.69 - 4.30: 11372 4.30 - 4.90: 17532 Nonbonded interactions: 39101 Sorted by model distance: nonbonded pdb="MG MG G2002 " pdb=" F3 ALF G2003 " model vdw 1.879 2.120 nonbonded pdb=" O2B ADP G2001 " pdb="MG MG G2002 " model vdw 2.007 2.170 nonbonded pdb=" N2 DG K 40 " pdb=" O2 DC L -40 " model vdw 2.323 2.520 nonbonded pdb=" O TYR G 975 " pdb=" NH1 ARG G1201 " model vdw 2.327 2.520 nonbonded pdb=" NH2 ARG G1608 " pdb=" OP2 DC L -28 " model vdw 2.366 2.520 ... (remaining 39096 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=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: 2.610 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: 9.490 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 19.460 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 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 : 0.010 0.115 4693 Z= 0.594 Angle : 1.701 70.061 6512 Z= 0.727 Chirality : 0.064 0.267 720 Planarity : 0.013 0.140 667 Dihedral : 20.609 164.056 1865 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.37), residues: 431 helix: -1.96 (0.28), residues: 215 sheet: -0.20 (0.76), residues: 54 loop : -0.88 (0.50), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.004 TRP G1650 HIS 0.011 0.002 HIS G1663 PHE 0.039 0.005 PHE G1079 TYR 0.025 0.006 TYR G1588 ARG 0.036 0.004 ARG G1201 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.417 Fit side-chains revert: symmetry clash REVERT: G 1001 LEU cc_start: 0.8600 (mt) cc_final: 0.8312 (mm) REVERT: G 1020 ILE cc_start: 0.7443 (mm) cc_final: 0.7217 (mt) REVERT: G 1143 MET cc_start: 0.8052 (mmp) cc_final: 0.7527 (mmt) REVERT: G 1186 GLN cc_start: 0.5578 (pm20) cc_final: 0.5134 (tt0) REVERT: G 1224 TYR cc_start: 0.7796 (p90) cc_final: 0.7327 (p90) REVERT: G 1240 MET cc_start: 0.7127 (mmm) cc_final: 0.6864 (mmt) REVERT: G 1585 MET cc_start: 0.8656 (tpt) cc_final: 0.8376 (tpp) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.2863 time to fit residues: 38.6887 Evaluate side-chains 63 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 39 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 19 optimal weight: 0.0870 chunk 12 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 42 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G1663 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4693 Z= 0.243 Angle : 0.649 9.066 6512 Z= 0.339 Chirality : 0.039 0.147 720 Planarity : 0.004 0.047 667 Dihedral : 24.282 116.077 947 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.01 % Allowed : 7.56 % Favored : 91.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.82 (0.40), residues: 431 helix: -0.70 (0.32), residues: 221 sheet: -0.02 (0.68), residues: 65 loop : -0.17 (0.55), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP G1650 HIS 0.003 0.001 HIS G1663 PHE 0.015 0.002 PHE G1264 TYR 0.009 0.001 TYR G 975 ARG 0.003 0.001 ARG G1063 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 72 time to evaluate : 0.414 Fit side-chains revert: symmetry clash REVERT: G 1001 LEU cc_start: 0.8673 (mt) cc_final: 0.8422 (mm) REVERT: G 1143 MET cc_start: 0.8004 (mmp) cc_final: 0.7435 (mmt) REVERT: G 1186 GLN cc_start: 0.5231 (pm20) cc_final: 0.4517 (pt0) REVERT: G 1224 TYR cc_start: 0.7690 (p90) cc_final: 0.7324 (p90) REVERT: G 1688 LYS cc_start: 0.7610 (OUTLIER) cc_final: 0.7108 (tttp) outliers start: 4 outliers final: 2 residues processed: 75 average time/residue: 0.2145 time to fit residues: 19.6411 Evaluate side-chains 63 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 60 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 1076 ASP Chi-restraints excluded: chain G residue 1602 SER Chi-restraints excluded: chain G residue 1688 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 13 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 42 optimal weight: 0.2980 chunk 46 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G1140 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 4693 Z= 0.273 Angle : 0.626 6.764 6512 Z= 0.328 Chirality : 0.039 0.137 720 Planarity : 0.004 0.029 667 Dihedral : 24.132 114.961 947 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.76 % Allowed : 12.09 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.55 (0.40), residues: 431 helix: -0.38 (0.33), residues: 221 sheet: 0.04 (0.68), residues: 65 loop : -0.20 (0.54), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP G1650 HIS 0.004 0.001 HIS G1191 PHE 0.012 0.002 PHE G1264 TYR 0.012 0.001 TYR G 975 ARG 0.006 0.001 ARG G1679 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 59 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 1001 LEU cc_start: 0.8744 (mt) cc_final: 0.8491 (mm) REVERT: G 1143 MET cc_start: 0.7963 (mmp) cc_final: 0.7404 (mmt) REVERT: G 1189 ARG cc_start: 0.7361 (mtm110) cc_final: 0.7039 (ptt90) REVERT: G 1240 MET cc_start: 0.6139 (mmt) cc_final: 0.5724 (mpp) REVERT: G 1585 MET cc_start: 0.8600 (tpt) cc_final: 0.8389 (tpp) outliers start: 7 outliers final: 4 residues processed: 64 average time/residue: 0.2402 time to fit residues: 18.5905 Evaluate side-chains 60 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 56 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 991 ILE Chi-restraints excluded: chain G residue 1076 ASP Chi-restraints excluded: chain G residue 1602 SER Chi-restraints excluded: chain G residue 1648 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 4 optimal weight: 0.6980 chunk 20 optimal weight: 0.0020 chunk 28 optimal weight: 0.0980 chunk 42 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 22 optimal weight: 0.4980 chunk 40 optimal weight: 0.7980 chunk 12 optimal weight: 0.4980 chunk 37 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 overall best weight: 0.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G1186 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.3803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4693 Z= 0.182 Angle : 0.549 6.343 6512 Z= 0.289 Chirality : 0.036 0.125 720 Planarity : 0.003 0.026 667 Dihedral : 23.873 112.774 947 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.76 % Allowed : 12.85 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.19 (0.40), residues: 431 helix: -0.03 (0.33), residues: 221 sheet: 0.29 (0.67), residues: 65 loop : -0.17 (0.55), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G1147 HIS 0.004 0.001 HIS G1191 PHE 0.009 0.001 PHE G1219 TYR 0.007 0.001 TYR G 975 ARG 0.004 0.000 ARG G1679 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 61 time to evaluate : 0.421 Fit side-chains revert: symmetry clash REVERT: G 1001 LEU cc_start: 0.8669 (mt) cc_final: 0.8458 (mm) REVERT: G 1143 MET cc_start: 0.7813 (mmp) cc_final: 0.7382 (mmt) REVERT: G 1189 ARG cc_start: 0.7376 (mtm110) cc_final: 0.7043 (ptt90) REVERT: G 1224 TYR cc_start: 0.7917 (p90) cc_final: 0.7664 (p90) REVERT: G 1240 MET cc_start: 0.6221 (mmt) cc_final: 0.5899 (mpp) outliers start: 7 outliers final: 5 residues processed: 68 average time/residue: 0.2085 time to fit residues: 17.4838 Evaluate side-chains 59 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 54 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 1076 ASP Chi-restraints excluded: chain G residue 1100 LYS Chi-restraints excluded: chain G residue 1186 GLN Chi-restraints excluded: chain G residue 1602 SER Chi-restraints excluded: chain G residue 1648 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 33 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G1097 GLN G1151 HIS ** G1692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.3943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 4693 Z= 0.293 Angle : 0.607 7.128 6512 Z= 0.318 Chirality : 0.038 0.130 720 Planarity : 0.004 0.032 667 Dihedral : 23.894 112.451 947 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.51 % Allowed : 14.11 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.40), residues: 431 helix: -0.22 (0.33), residues: 220 sheet: -0.03 (0.65), residues: 65 loop : -0.23 (0.54), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP G1650 HIS 0.004 0.001 HIS G1191 PHE 0.020 0.002 PHE G1615 TYR 0.012 0.001 TYR G 975 ARG 0.003 0.000 ARG G1608 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 58 time to evaluate : 0.475 Fit side-chains revert: symmetry clash REVERT: G 966 LYS cc_start: 0.8382 (mmmt) cc_final: 0.7807 (tptp) REVERT: G 1001 LEU cc_start: 0.8779 (mt) cc_final: 0.8520 (mm) REVERT: G 1091 SER cc_start: 0.8579 (t) cc_final: 0.8228 (p) REVERT: G 1143 MET cc_start: 0.7848 (mmp) cc_final: 0.7413 (mmt) REVERT: G 1189 ARG cc_start: 0.7365 (mtm110) cc_final: 0.7104 (ptt-90) REVERT: G 1224 TYR cc_start: 0.7920 (p90) cc_final: 0.7668 (p90) outliers start: 6 outliers final: 5 residues processed: 64 average time/residue: 0.2359 time to fit residues: 18.2862 Evaluate side-chains 59 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 54 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 968 LEU Chi-restraints excluded: chain G residue 1076 ASP Chi-restraints excluded: chain G residue 1100 LYS Chi-restraints excluded: chain G residue 1602 SER Chi-restraints excluded: chain G residue 1648 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 11 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 21 optimal weight: 0.4980 chunk 3 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G1097 GLN G1186 GLN ** G1692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.4123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 4693 Z= 0.298 Angle : 0.612 6.775 6512 Z= 0.319 Chirality : 0.039 0.134 720 Planarity : 0.004 0.030 667 Dihedral : 23.825 113.036 947 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.02 % Allowed : 13.10 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.72 (0.39), residues: 431 helix: -0.30 (0.33), residues: 219 sheet: -0.35 (0.62), residues: 67 loop : -0.52 (0.52), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP G1036 HIS 0.003 0.001 HIS G1191 PHE 0.017 0.002 PHE G1219 TYR 0.010 0.001 TYR G 975 ARG 0.004 0.001 ARG G1679 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 64 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 966 LYS cc_start: 0.8387 (mmmt) cc_final: 0.7826 (tptp) REVERT: G 1091 SER cc_start: 0.8559 (t) cc_final: 0.8220 (p) REVERT: G 1098 LYS cc_start: 0.8035 (mttt) cc_final: 0.7834 (mttp) REVERT: G 1143 MET cc_start: 0.7861 (mmp) cc_final: 0.7416 (mmt) REVERT: G 1189 ARG cc_start: 0.7386 (mtm110) cc_final: 0.7040 (ptt-90) REVERT: G 1224 TYR cc_start: 0.7814 (p90) cc_final: 0.7599 (p90) REVERT: G 1240 MET cc_start: 0.6770 (mpp) cc_final: 0.6467 (mpp) REVERT: G 1669 LYS cc_start: 0.8536 (mttm) cc_final: 0.8328 (mtmt) outliers start: 12 outliers final: 9 residues processed: 72 average time/residue: 0.2355 time to fit residues: 20.5103 Evaluate side-chains 66 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 57 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 1032 THR Chi-restraints excluded: chain G residue 1076 ASP Chi-restraints excluded: chain G residue 1100 LYS Chi-restraints excluded: chain G residue 1107 ASP Chi-restraints excluded: chain G residue 1217 ASP Chi-restraints excluded: chain G residue 1258 MET Chi-restraints excluded: chain G residue 1602 SER Chi-restraints excluded: chain G residue 1648 SER Chi-restraints excluded: chain G residue 1691 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 25 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 28 optimal weight: 0.0770 chunk 27 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G1097 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.4307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4693 Z= 0.259 Angle : 0.589 6.577 6512 Z= 0.307 Chirality : 0.038 0.148 720 Planarity : 0.004 0.030 667 Dihedral : 23.675 112.278 947 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.52 % Allowed : 14.61 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.66 (0.39), residues: 431 helix: -0.20 (0.33), residues: 221 sheet: -0.35 (0.62), residues: 67 loop : -0.56 (0.53), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP G1036 HIS 0.003 0.001 HIS G1191 PHE 0.016 0.002 PHE G1219 TYR 0.008 0.001 TYR G1591 ARG 0.003 0.000 ARG G1679 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 59 time to evaluate : 0.468 Fit side-chains REVERT: G 966 LYS cc_start: 0.8382 (mmmt) cc_final: 0.7821 (tptp) REVERT: G 1091 SER cc_start: 0.8566 (t) cc_final: 0.8229 (p) REVERT: G 1143 MET cc_start: 0.7860 (mmp) cc_final: 0.7413 (mmt) REVERT: G 1189 ARG cc_start: 0.7360 (mtm110) cc_final: 0.7037 (ptt-90) REVERT: G 1669 LYS cc_start: 0.8516 (mttm) cc_final: 0.8310 (mtmt) outliers start: 10 outliers final: 8 residues processed: 67 average time/residue: 0.2331 time to fit residues: 18.9983 Evaluate side-chains 60 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 52 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 1032 THR Chi-restraints excluded: chain G residue 1076 ASP Chi-restraints excluded: chain G residue 1100 LYS Chi-restraints excluded: chain G residue 1217 ASP Chi-restraints excluded: chain G residue 1220 CYS Chi-restraints excluded: chain G residue 1258 MET Chi-restraints excluded: chain G residue 1602 SER Chi-restraints excluded: chain G residue 1648 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 4 optimal weight: 0.5980 chunk 35 optimal weight: 0.3980 chunk 41 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 42 optimal weight: 0.3980 chunk 25 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 12 optimal weight: 0.4980 chunk 38 optimal weight: 0.8980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G1097 GLN G1692 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.4490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 4693 Z= 0.219 Angle : 0.567 6.639 6512 Z= 0.294 Chirality : 0.036 0.135 720 Planarity : 0.003 0.030 667 Dihedral : 23.448 111.503 947 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.52 % Allowed : 14.86 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.58 (0.39), residues: 431 helix: -0.06 (0.34), residues: 220 sheet: -0.45 (0.60), residues: 67 loop : -0.57 (0.53), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP G1036 HIS 0.002 0.000 HIS G1191 PHE 0.021 0.002 PHE G1615 TYR 0.009 0.001 TYR G1224 ARG 0.003 0.000 ARG G1679 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 55 time to evaluate : 0.482 Fit side-chains REVERT: G 966 LYS cc_start: 0.8332 (mmmt) cc_final: 0.7775 (tptp) REVERT: G 1091 SER cc_start: 0.8557 (t) cc_final: 0.8258 (p) REVERT: G 1143 MET cc_start: 0.7858 (mmp) cc_final: 0.7406 (mmt) REVERT: G 1189 ARG cc_start: 0.7364 (mtm110) cc_final: 0.7048 (ptt90) REVERT: G 1240 MET cc_start: 0.6663 (mpp) cc_final: 0.6196 (mmt) outliers start: 10 outliers final: 9 residues processed: 64 average time/residue: 0.2294 time to fit residues: 17.7964 Evaluate side-chains 61 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 52 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 991 ILE Chi-restraints excluded: chain G residue 1032 THR Chi-restraints excluded: chain G residue 1076 ASP Chi-restraints excluded: chain G residue 1100 LYS Chi-restraints excluded: chain G residue 1217 ASP Chi-restraints excluded: chain G residue 1220 CYS Chi-restraints excluded: chain G residue 1258 MET Chi-restraints excluded: chain G residue 1602 SER Chi-restraints excluded: chain G residue 1648 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 39 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G1097 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.4514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 4693 Z= 0.292 Angle : 0.613 6.978 6512 Z= 0.315 Chirality : 0.039 0.145 720 Planarity : 0.004 0.029 667 Dihedral : 23.410 111.280 947 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.77 % Allowed : 15.37 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.77 (0.39), residues: 431 helix: -0.23 (0.33), residues: 220 sheet: -0.54 (0.61), residues: 67 loop : -0.63 (0.52), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP G1036 HIS 0.003 0.001 HIS G1191 PHE 0.020 0.002 PHE G1615 TYR 0.008 0.001 TYR G1224 ARG 0.003 0.000 ARG G1608 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 53 time to evaluate : 0.433 Fit side-chains REVERT: G 966 LYS cc_start: 0.8341 (mmmt) cc_final: 0.7783 (tptp) REVERT: G 1091 SER cc_start: 0.8539 (t) cc_final: 0.8250 (p) REVERT: G 1143 MET cc_start: 0.7890 (mmp) cc_final: 0.7416 (mmt) REVERT: G 1189 ARG cc_start: 0.7358 (mtm110) cc_final: 0.7046 (ptt-90) REVERT: G 1240 MET cc_start: 0.6663 (mpp) cc_final: 0.6230 (mmt) outliers start: 11 outliers final: 9 residues processed: 61 average time/residue: 0.2147 time to fit residues: 16.0967 Evaluate side-chains 60 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 51 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 991 ILE Chi-restraints excluded: chain G residue 1032 THR Chi-restraints excluded: chain G residue 1076 ASP Chi-restraints excluded: chain G residue 1100 LYS Chi-restraints excluded: chain G residue 1217 ASP Chi-restraints excluded: chain G residue 1220 CYS Chi-restraints excluded: chain G residue 1258 MET Chi-restraints excluded: chain G residue 1602 SER Chi-restraints excluded: chain G residue 1648 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 22 optimal weight: 0.8980 chunk 29 optimal weight: 0.0060 chunk 39 optimal weight: 0.9980 chunk 11 optimal weight: 0.2980 chunk 34 optimal weight: 0.7980 chunk 5 optimal weight: 0.4980 chunk 10 optimal weight: 0.3980 chunk 37 optimal weight: 0.2980 chunk 15 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 overall best weight: 0.2996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.4665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4693 Z= 0.178 Angle : 0.552 7.149 6512 Z= 0.286 Chirality : 0.035 0.130 720 Planarity : 0.003 0.030 667 Dihedral : 23.079 110.965 947 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.27 % Allowed : 15.62 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.42 (0.40), residues: 431 helix: 0.10 (0.34), residues: 220 sheet: -0.39 (0.62), residues: 67 loop : -0.57 (0.53), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP G1053 HIS 0.002 0.000 HIS G1191 PHE 0.020 0.001 PHE G1615 TYR 0.011 0.001 TYR G1224 ARG 0.003 0.000 ARG G1679 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 54 time to evaluate : 0.460 Fit side-chains REVERT: G 966 LYS cc_start: 0.8281 (mmmt) cc_final: 0.7731 (tptp) REVERT: G 1091 SER cc_start: 0.8569 (t) cc_final: 0.8267 (p) REVERT: G 1143 MET cc_start: 0.7832 (mmp) cc_final: 0.7423 (mmt) REVERT: G 1189 ARG cc_start: 0.7420 (mtm110) cc_final: 0.7066 (ptt90) outliers start: 9 outliers final: 8 residues processed: 62 average time/residue: 0.2381 time to fit residues: 17.8228 Evaluate side-chains 60 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 52 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 991 ILE Chi-restraints excluded: chain G residue 1032 THR Chi-restraints excluded: chain G residue 1100 LYS Chi-restraints excluded: chain G residue 1217 ASP Chi-restraints excluded: chain G residue 1220 CYS Chi-restraints excluded: chain G residue 1258 MET Chi-restraints excluded: chain G residue 1602 SER Chi-restraints excluded: chain G residue 1648 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 6 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 26 optimal weight: 0.3980 chunk 42 optimal weight: 0.3980 chunk 25 optimal weight: 1.9990 chunk 31 optimal weight: 0.3980 chunk 1 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G1097 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.104796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.092636 restraints weight = 7692.515| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 0.85 r_work: 0.3312 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.4692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 4693 Z= 0.220 Angle : 0.571 7.649 6512 Z= 0.295 Chirality : 0.036 0.135 720 Planarity : 0.003 0.030 667 Dihedral : 23.058 109.959 947 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.52 % Allowed : 15.11 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.46 (0.39), residues: 431 helix: 0.07 (0.34), residues: 219 sheet: -0.40 (0.62), residues: 67 loop : -0.58 (0.52), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP G1036 HIS 0.002 0.000 HIS G1191 PHE 0.019 0.002 PHE G1615 TYR 0.012 0.001 TYR G1018 ARG 0.003 0.000 ARG G1679 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1448.28 seconds wall clock time: 26 minutes 54.81 seconds (1614.81 seconds total)