Starting phenix.real_space_refine on Fri Jul 19 11:25:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tqm_41508/07_2024/8tqm_41508_neut_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tqm_41508/07_2024/8tqm_41508.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/8tqm_41508/07_2024/8tqm_41508.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tqm_41508/07_2024/8tqm_41508.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tqm_41508/07_2024/8tqm_41508_neut_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tqm_41508/07_2024/8tqm_41508_neut_trim.cif" } 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= 0.002 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 39 5.16 5 C 4906 2.51 5 N 1087 2.21 5 O 1195 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 7231 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 843, 6921 Classifications: {'peptide': 843} Link IDs: {'PTRANS': 31, 'TRANS': 811} Chain breaks: 5 Chain: "A" Number of atoms: 310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 310 Unusual residues: {'ERG': 1, 'PC1': 4, 'TGL': 1, 'Y01': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 33 Time building chain proxies: 5.27, per 1000 atoms: 0.73 Number of scatterers: 7231 At special positions: 0 Unit cell: (74.62, 102.83, 143.78, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 39 16.00 P 4 15.00 O 1195 8.00 N 1087 7.00 C 4906 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: 3.30 Conformation dependent library (CDL) restraints added in 1.4 seconds 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1608 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 2 sheets defined 80.1% alpha, 2.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 113 through 162 removed outlier: 4.629A pdb=" N VAL A 145 " --> pdb=" O TYR A 141 " (cutoff:3.500A) Proline residue: A 146 - end of helix Processing helix chain 'A' and resid 169 through 176 removed outlier: 3.582A pdb=" N SER A 173 " --> pdb=" O ASP A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 226 Processing helix chain 'A' and resid 226 through 238 removed outlier: 3.557A pdb=" N SER A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 522 removed outlier: 5.014A pdb=" N PHE A 493 " --> pdb=" O ILE A 489 " (cutoff:3.500A) Proline residue: A 494 - end of helix Processing helix chain 'A' and resid 545 through 563 Processing helix chain 'A' and resid 569 through 597 Proline residue: A 576 - end of helix removed outlier: 3.747A pdb=" N ASN A 593 " --> pdb=" O CYS A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 635 Processing helix chain 'A' and resid 635 through 649 Processing helix chain 'A' and resid 649 through 655 Processing helix chain 'A' and resid 662 through 667 Processing helix chain 'A' and resid 672 through 700 removed outlier: 3.916A pdb=" N PHE A 676 " --> pdb=" O PRO A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 726 Processing helix chain 'A' and resid 727 through 756 removed outlier: 4.383A pdb=" N HIS A 753 " --> pdb=" O GLY A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 774 Processing helix chain 'A' and resid 780 through 800 Processing helix chain 'A' and resid 802 through 823 Processing helix chain 'A' and resid 824 through 829 Processing helix chain 'A' and resid 833 through 836 Processing helix chain 'A' and resid 844 through 849 Processing helix chain 'A' and resid 851 through 859 Processing helix chain 'A' and resid 868 through 879 Processing helix chain 'A' and resid 902 through 907 removed outlier: 3.631A pdb=" N GLN A 907 " --> pdb=" O ARG A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 936 Processing helix chain 'A' and resid 960 through 995 Processing helix chain 'A' and resid 998 through 1007 removed outlier: 3.720A pdb=" N VAL A1002 " --> pdb=" O GLY A 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 1011 through 1025 Processing helix chain 'A' and resid 1029 through 1052 removed outlier: 4.537A pdb=" N LYS A1045 " --> pdb=" O SER A1041 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ASP A1046 " --> pdb=" O LYS A1042 " (cutoff:3.500A) Processing helix chain 'A' and resid 1096 through 1107 removed outlier: 3.700A pdb=" N SER A1107 " --> pdb=" O SER A1103 " (cutoff:3.500A) Processing helix chain 'A' and resid 1107 through 1137 Processing helix chain 'A' and resid 1137 through 1145 Processing helix chain 'A' and resid 1167 through 1195 removed outlier: 3.508A pdb=" N PHE A1193 " --> pdb=" O LEU A1189 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG A1194 " --> pdb=" O LYS A1190 " (cutoff:3.500A) Processing helix chain 'A' and resid 1199 through 1215 Processing helix chain 'A' and resid 1215 through 1230 removed outlier: 3.929A pdb=" N LEU A1224 " --> pdb=" O VAL A1220 " (cutoff:3.500A) Proline residue: A1225 - end of helix Processing helix chain 'A' and resid 1265 through 1293 Processing sheet with id=AA1, first strand: chain 'A' and resid 838 through 842 Processing sheet with id=AA2, first strand: chain 'A' and resid 912 through 913 removed outlier: 3.963A pdb=" N LEU A 892 " --> pdb=" O VAL A 913 " (cutoff:3.500A) 521 hydrogen bonds defined for protein. 1551 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.10 Time building geometry restraints manager: 3.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1401 1.33 - 1.45: 1788 1.45 - 1.57: 4156 1.57 - 1.69: 11 1.69 - 1.81: 67 Bond restraints: 7423 Sorted by residual: bond pdb=" C21 PC1 A1401 " pdb=" O21 PC1 A1401 " ideal model delta sigma weight residual 1.331 1.460 -0.129 2.00e-02 2.50e+03 4.19e+01 bond pdb=" C21 PC1 A1404 " pdb=" O21 PC1 A1404 " ideal model delta sigma weight residual 1.331 1.455 -0.124 2.00e-02 2.50e+03 3.82e+01 bond pdb=" OG3 TGL A1403 " pdb=" CC1 TGL A1403 " ideal model delta sigma weight residual 1.332 1.454 -0.122 2.00e-02 2.50e+03 3.74e+01 bond pdb=" C21 PC1 A1402 " pdb=" O21 PC1 A1402 " ideal model delta sigma weight residual 1.331 1.453 -0.122 2.00e-02 2.50e+03 3.73e+01 bond pdb=" C31 PC1 A1402 " pdb=" O31 PC1 A1402 " ideal model delta sigma weight residual 1.330 1.449 -0.119 2.00e-02 2.50e+03 3.57e+01 ... (remaining 7418 not shown) Histogram of bond angle deviations from ideal: 93.86 - 102.35: 32 102.35 - 110.85: 2720 110.85 - 119.34: 3411 119.34 - 127.84: 3798 127.84 - 136.33: 62 Bond angle restraints: 10023 Sorted by residual: angle pdb=" N PC1 A1401 " pdb=" C12 PC1 A1401 " pdb=" C11 PC1 A1401 " ideal model delta sigma weight residual 115.31 136.33 -21.02 3.00e+00 1.11e-01 4.91e+01 angle pdb=" C LYS A 698 " pdb=" N ASN A 699 " pdb=" CA ASN A 699 " ideal model delta sigma weight residual 122.58 110.83 11.75 2.07e+00 2.33e-01 3.22e+01 angle pdb=" CAM Y01 A1406 " pdb=" CAY Y01 A1406 " pdb=" OAW Y01 A1406 " ideal model delta sigma weight residual 111.19 126.14 -14.95 3.00e+00 1.11e-01 2.48e+01 angle pdb=" CA1 TGL A1403 " pdb=" CA2 TGL A1403 " pdb=" CA3 TGL A1403 " ideal model delta sigma weight residual 113.86 128.69 -14.83 3.00e+00 1.11e-01 2.44e+01 angle pdb=" CA LYS A 804 " pdb=" C LYS A 804 " pdb=" N PRO A 805 " ideal model delta sigma weight residual 120.77 117.34 3.43 9.70e-01 1.06e+00 1.25e+01 ... (remaining 10018 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.88: 3933 13.88 - 27.77: 385 27.77 - 41.65: 132 41.65 - 55.54: 43 55.54 - 69.42: 13 Dihedral angle restraints: 4506 sinusoidal: 2011 harmonic: 2495 Sorted by residual: dihedral pdb=" CA ARG A 964 " pdb=" CB ARG A 964 " pdb=" CG ARG A 964 " pdb=" CD ARG A 964 " ideal model delta sinusoidal sigma weight residual -60.00 -113.15 53.15 3 1.50e+01 4.44e-03 9.18e+00 dihedral pdb=" CA TYR A1222 " pdb=" C TYR A1222 " pdb=" N VAL A1223 " pdb=" CA VAL A1223 " ideal model delta harmonic sigma weight residual -180.00 -165.43 -14.57 0 5.00e+00 4.00e-02 8.49e+00 dihedral pdb=" CA LYS A 933 " pdb=" CB LYS A 933 " pdb=" CG LYS A 933 " pdb=" CD LYS A 933 " ideal model delta sinusoidal sigma weight residual 180.00 132.69 47.31 3 1.50e+01 4.44e-03 8.47e+00 ... (remaining 4503 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 1079 0.091 - 0.182: 39 0.182 - 0.272: 3 0.272 - 0.363: 1 0.363 - 0.454: 1 Chirality restraints: 1123 Sorted by residual: chirality pdb=" CBH Y01 A1406 " pdb=" CAT Y01 A1406 " pdb=" CAZ Y01 A1406 " pdb=" CBF Y01 A1406 " both_signs ideal model delta sigma weight residual False -2.85 -2.40 -0.45 2.00e-01 2.50e+01 5.15e+00 chirality pdb=" CBG Y01 A1406 " pdb=" CAQ Y01 A1406 " pdb=" CBD Y01 A1406 " pdb=" CBI Y01 A1406 " both_signs ideal model delta sigma weight residual False -2.33 -2.68 0.35 2.00e-01 2.50e+01 3.06e+00 chirality pdb=" CBF Y01 A1406 " pdb=" CAS Y01 A1406 " pdb=" CBD Y01 A1406 " pdb=" CBH Y01 A1406 " both_signs ideal model delta sigma weight residual False -2.45 -2.70 0.26 2.00e-01 2.50e+01 1.63e+00 ... (remaining 1120 not shown) Planarity restraints: 1170 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 671 " -0.031 5.00e-02 4.00e+02 4.66e-02 3.48e+00 pdb=" N PRO A 672 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 672 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 672 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A1000 " -0.029 5.00e-02 4.00e+02 4.31e-02 2.98e+00 pdb=" N PRO A1001 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO A1001 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A1001 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 632 " 0.009 2.00e-02 2.50e+03 1.72e-02 2.96e+00 pdb=" C ILE A 632 " -0.030 2.00e-02 2.50e+03 pdb=" O ILE A 632 " 0.011 2.00e-02 2.50e+03 pdb=" N GLU A 633 " 0.010 2.00e-02 2.50e+03 ... (remaining 1167 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.36: 16 2.36 - 2.99: 3984 2.99 - 3.63: 10885 3.63 - 4.26: 16156 4.26 - 4.90: 27239 Nonbonded interactions: 58280 Sorted by model distance: nonbonded pdb=" NH2 ARG A 734 " pdb=" NH2 ARG A 903 " model vdw 1.724 3.200 nonbonded pdb=" NH1 ARG A 734 " pdb=" NH1 ARG A 903 " model vdw 1.911 3.200 nonbonded pdb=" OG SER A1024 " pdb=" OD1 ASN A1029 " model vdw 2.118 2.440 nonbonded pdb=" ND2 ASN A 699 " pdb=" OE2 GLU A 808 " model vdw 2.212 2.520 nonbonded pdb=" NE2 HIS A 213 " pdb=" O1 ERG A1407 " model vdw 2.264 2.520 ... (remaining 58275 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=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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.560 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 24.270 Find NCS groups from input model: 0.070 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.129 7423 Z= 0.398 Angle : 0.919 21.021 10023 Z= 0.410 Chirality : 0.045 0.454 1123 Planarity : 0.004 0.047 1170 Dihedral : 13.425 69.421 2898 Min Nonbonded Distance : 1.724 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.30), residues: 831 helix: 2.24 (0.20), residues: 651 sheet: -1.21 (1.11), residues: 22 loop : -1.24 (0.50), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 149 HIS 0.007 0.001 HIS A1049 PHE 0.028 0.001 PHE A1171 TYR 0.016 0.001 TYR A 505 ARG 0.006 0.001 ARG A 597 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 0.844 Fit side-chains REVERT: A 820 ARG cc_start: 0.8121 (tmm-80) cc_final: 0.7840 (ttp-110) REVERT: A 1219 MET cc_start: 0.7316 (mmm) cc_final: 0.6987 (tpt) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.2215 time to fit residues: 39.2891 Evaluate side-chains 92 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 65 optimal weight: 0.0270 chunk 25 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 49 optimal weight: 10.0000 chunk 76 optimal weight: 2.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 721 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7423 Z= 0.212 Angle : 0.547 7.589 10023 Z= 0.275 Chirality : 0.039 0.148 1123 Planarity : 0.004 0.052 1170 Dihedral : 12.601 75.072 1278 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.65 % Allowed : 7.07 % Favored : 92.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.29), residues: 831 helix: 2.29 (0.20), residues: 658 sheet: -1.56 (1.05), residues: 22 loop : -1.09 (0.50), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 149 HIS 0.003 0.001 HIS A 721 PHE 0.016 0.001 PHE A 614 TYR 0.030 0.001 TYR A 965 ARG 0.002 0.000 ARG A 964 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 98 time to evaluate : 0.785 Fit side-chains REVERT: A 175 ILE cc_start: 0.8504 (mm) cc_final: 0.8159 (mt) REVERT: A 835 THR cc_start: 0.8697 (t) cc_final: 0.8264 (m) outliers start: 5 outliers final: 4 residues processed: 101 average time/residue: 0.1907 time to fit residues: 26.2669 Evaluate side-chains 92 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 88 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 1103 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 0.4980 chunk 23 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 82 optimal weight: 20.0000 chunk 68 optimal weight: 1.9990 chunk 75 optimal weight: 8.9990 chunk 26 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 721 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 GLN ** A 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7423 Z= 0.247 Angle : 0.539 7.304 10023 Z= 0.273 Chirality : 0.039 0.144 1123 Planarity : 0.004 0.053 1170 Dihedral : 12.397 80.157 1278 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.05 % Allowed : 8.77 % Favored : 90.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.29), residues: 831 helix: 2.19 (0.20), residues: 659 sheet: -1.69 (1.04), residues: 22 loop : -1.11 (0.49), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 149 HIS 0.005 0.001 HIS A 721 PHE 0.015 0.001 PHE A 614 TYR 0.027 0.001 TYR A 965 ARG 0.004 0.000 ARG A 225 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 94 time to evaluate : 0.796 Fit side-chains REVERT: A 175 ILE cc_start: 0.8620 (mm) cc_final: 0.8316 (mt) REVERT: A 835 THR cc_start: 0.8678 (t) cc_final: 0.8208 (m) outliers start: 8 outliers final: 3 residues processed: 98 average time/residue: 0.1709 time to fit residues: 24.0395 Evaluate side-chains 88 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 85 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 897 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 81 optimal weight: 30.0000 chunk 40 optimal weight: 0.6980 chunk 72 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 721 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 946 ASN ** A1181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7423 Z= 0.218 Angle : 0.511 7.138 10023 Z= 0.260 Chirality : 0.038 0.143 1123 Planarity : 0.004 0.054 1170 Dihedral : 12.284 79.789 1278 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.44 % Allowed : 9.95 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.38 (0.29), residues: 831 helix: 2.24 (0.20), residues: 660 sheet: -1.49 (1.07), residues: 22 loop : -0.99 (0.50), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 662 HIS 0.006 0.001 HIS A 721 PHE 0.013 0.001 PHE A 614 TYR 0.024 0.001 TYR A 965 ARG 0.003 0.000 ARG A 225 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 90 time to evaluate : 0.828 Fit side-chains REVERT: A 175 ILE cc_start: 0.8630 (mm) cc_final: 0.8363 (mt) REVERT: A 1015 VAL cc_start: 0.8199 (t) cc_final: 0.7825 (m) outliers start: 11 outliers final: 6 residues processed: 97 average time/residue: 0.1596 time to fit residues: 22.7874 Evaluate side-chains 92 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 86 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 897 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 1.9990 chunk 46 optimal weight: 0.4980 chunk 1 optimal weight: 6.9990 chunk 60 optimal weight: 0.4980 chunk 33 optimal weight: 0.9980 chunk 69 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 41 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 716 ASN ** A 721 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 946 ASN A1181 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7423 Z= 0.206 Angle : 0.498 6.540 10023 Z= 0.253 Chirality : 0.037 0.140 1123 Planarity : 0.004 0.054 1170 Dihedral : 12.119 80.668 1278 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.57 % Allowed : 10.86 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.29), residues: 831 helix: 2.28 (0.20), residues: 660 sheet: -1.54 (1.08), residues: 22 loop : -0.94 (0.50), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 662 HIS 0.003 0.001 HIS A 721 PHE 0.012 0.001 PHE A 614 TYR 0.023 0.001 TYR A 965 ARG 0.003 0.000 ARG A 702 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 89 time to evaluate : 0.821 Fit side-chains REVERT: A 175 ILE cc_start: 0.8597 (mm) cc_final: 0.8342 (mt) REVERT: A 1015 VAL cc_start: 0.8199 (t) cc_final: 0.7828 (m) REVERT: A 1106 ASP cc_start: 0.7264 (m-30) cc_final: 0.7013 (m-30) REVERT: A 1266 MET cc_start: 0.5406 (ppp) cc_final: 0.5034 (ppp) outliers start: 12 outliers final: 7 residues processed: 95 average time/residue: 0.1524 time to fit residues: 21.1610 Evaluate side-chains 93 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 86 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 644 MET Chi-restraints excluded: chain A residue 897 SER Chi-restraints excluded: chain A residue 1103 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 0.5980 chunk 73 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 81 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN ** A 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7423 Z= 0.217 Angle : 0.499 6.648 10023 Z= 0.254 Chirality : 0.038 0.142 1123 Planarity : 0.004 0.054 1170 Dihedral : 12.004 80.936 1278 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.44 % Allowed : 11.65 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.29), residues: 831 helix: 2.27 (0.20), residues: 661 sheet: -1.57 (1.10), residues: 22 loop : -1.03 (0.50), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 662 HIS 0.003 0.001 HIS A1218 PHE 0.013 0.001 PHE A 614 TYR 0.023 0.001 TYR A 965 ARG 0.003 0.000 ARG A1126 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 87 time to evaluate : 0.784 Fit side-chains REVERT: A 175 ILE cc_start: 0.8623 (mm) cc_final: 0.8379 (mt) REVERT: A 1106 ASP cc_start: 0.7280 (m-30) cc_final: 0.7022 (m-30) REVERT: A 1266 MET cc_start: 0.5387 (ppp) cc_final: 0.4684 (ppp) outliers start: 11 outliers final: 8 residues processed: 92 average time/residue: 0.1619 time to fit residues: 21.6187 Evaluate side-chains 93 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 85 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 897 SER Chi-restraints excluded: chain A residue 915 LYS Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1218 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 59 optimal weight: 0.0270 chunk 45 optimal weight: 0.5980 chunk 68 optimal weight: 0.5980 chunk 80 optimal weight: 9.9990 chunk 50 optimal weight: 8.9990 chunk 49 optimal weight: 6.9990 chunk 37 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7423 Z= 0.178 Angle : 0.477 6.682 10023 Z= 0.244 Chirality : 0.037 0.139 1123 Planarity : 0.004 0.054 1170 Dihedral : 11.747 82.654 1278 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.44 % Allowed : 11.91 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.29), residues: 831 helix: 2.36 (0.20), residues: 660 sheet: -0.79 (1.09), residues: 26 loop : -1.24 (0.50), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 662 HIS 0.003 0.001 HIS A 721 PHE 0.012 0.001 PHE A 614 TYR 0.021 0.001 TYR A 965 ARG 0.005 0.000 ARG A 710 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 89 time to evaluate : 0.821 Fit side-chains REVERT: A 175 ILE cc_start: 0.8603 (mm) cc_final: 0.8359 (mt) REVERT: A 963 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7656 (mm) REVERT: A 1106 ASP cc_start: 0.7205 (m-30) cc_final: 0.6972 (m-30) REVERT: A 1266 MET cc_start: 0.5385 (ppp) cc_final: 0.4759 (ppp) outliers start: 11 outliers final: 9 residues processed: 95 average time/residue: 0.1548 time to fit residues: 21.7200 Evaluate side-chains 96 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 86 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 644 MET Chi-restraints excluded: chain A residue 897 SER Chi-restraints excluded: chain A residue 915 LYS Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1218 HIS Chi-restraints excluded: chain A residue 1219 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 51 optimal weight: 6.9990 chunk 55 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 7 optimal weight: 0.0030 chunk 63 optimal weight: 0.4980 chunk 73 optimal weight: 8.9990 chunk 77 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 932 ASN ** A 945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7423 Z= 0.189 Angle : 0.487 6.724 10023 Z= 0.249 Chirality : 0.037 0.139 1123 Planarity : 0.004 0.054 1170 Dihedral : 11.642 88.147 1278 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.70 % Allowed : 11.78 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.29), residues: 831 helix: 2.37 (0.20), residues: 660 sheet: -0.90 (1.09), residues: 26 loop : -1.25 (0.50), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 662 HIS 0.003 0.001 HIS A 549 PHE 0.012 0.001 PHE A 614 TYR 0.021 0.001 TYR A 965 ARG 0.002 0.000 ARG A 702 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 87 time to evaluate : 0.783 Fit side-chains REVERT: A 175 ILE cc_start: 0.8606 (mm) cc_final: 0.8364 (mt) REVERT: A 963 LEU cc_start: 0.7925 (mm) cc_final: 0.7670 (mm) REVERT: A 1266 MET cc_start: 0.5368 (ppp) cc_final: 0.4764 (ppp) outliers start: 13 outliers final: 10 residues processed: 94 average time/residue: 0.1555 time to fit residues: 21.2649 Evaluate side-chains 94 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 84 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 695 MET Chi-restraints excluded: chain A residue 897 SER Chi-restraints excluded: chain A residue 915 LYS Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1218 HIS Chi-restraints excluded: chain A residue 1219 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 59 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 49 optimal weight: 10.0000 chunk 79 optimal weight: 0.4980 chunk 48 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7423 Z= 0.206 Angle : 0.496 6.782 10023 Z= 0.255 Chirality : 0.038 0.140 1123 Planarity : 0.004 0.054 1170 Dihedral : 11.601 87.153 1278 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.31 % Allowed : 12.17 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.48 (0.29), residues: 831 helix: 2.33 (0.20), residues: 660 sheet: -0.92 (1.10), residues: 26 loop : -1.24 (0.50), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 662 HIS 0.003 0.001 HIS A 721 PHE 0.013 0.001 PHE A 614 TYR 0.021 0.001 TYR A 965 ARG 0.002 0.000 ARG A 702 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 84 time to evaluate : 0.871 Fit side-chains REVERT: A 175 ILE cc_start: 0.8601 (mm) cc_final: 0.8363 (mt) REVERT: A 963 LEU cc_start: 0.7926 (mm) cc_final: 0.7683 (mm) REVERT: A 1266 MET cc_start: 0.5474 (ppp) cc_final: 0.4845 (ppp) outliers start: 10 outliers final: 9 residues processed: 90 average time/residue: 0.1991 time to fit residues: 26.3761 Evaluate side-chains 91 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 82 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 897 SER Chi-restraints excluded: chain A residue 915 LYS Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1218 HIS Chi-restraints excluded: chain A residue 1219 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 0.4980 chunk 55 optimal weight: 0.9990 chunk 83 optimal weight: 6.9990 chunk 77 optimal weight: 0.0970 chunk 66 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 52 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7423 Z= 0.212 Angle : 0.503 7.018 10023 Z= 0.257 Chirality : 0.038 0.140 1123 Planarity : 0.004 0.053 1170 Dihedral : 11.509 85.994 1278 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.05 % Allowed : 12.70 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.29), residues: 831 helix: 2.32 (0.20), residues: 660 sheet: -0.82 (1.12), residues: 26 loop : -1.29 (0.50), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 662 HIS 0.003 0.001 HIS A 721 PHE 0.013 0.001 PHE A 614 TYR 0.022 0.001 TYR A 965 ARG 0.002 0.000 ARG A 702 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 82 time to evaluate : 0.766 Fit side-chains REVERT: A 175 ILE cc_start: 0.8605 (mm) cc_final: 0.8364 (mt) REVERT: A 963 LEU cc_start: 0.7913 (mm) cc_final: 0.7679 (mm) REVERT: A 1266 MET cc_start: 0.5464 (ppp) cc_final: 0.4897 (ppp) outliers start: 8 outliers final: 8 residues processed: 87 average time/residue: 0.1626 time to fit residues: 20.6911 Evaluate side-chains 88 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 80 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 915 LYS Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1218 HIS Chi-restraints excluded: chain A residue 1219 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 66 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 12 optimal weight: 0.2980 chunk 58 optimal weight: 0.1980 chunk 3 optimal weight: 0.1980 chunk 48 optimal weight: 3.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.192765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.140630 restraints weight = 7658.226| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.85 r_work: 0.2949 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7423 Z= 0.160 Angle : 0.475 6.707 10023 Z= 0.245 Chirality : 0.037 0.142 1123 Planarity : 0.004 0.055 1170 Dihedral : 11.009 85.762 1278 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.92 % Allowed : 12.70 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.64 (0.30), residues: 831 helix: 2.46 (0.20), residues: 658 sheet: -0.82 (1.12), residues: 26 loop : -1.19 (0.50), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 662 HIS 0.002 0.000 HIS A 721 PHE 0.011 0.001 PHE A 614 TYR 0.020 0.001 TYR A 965 ARG 0.002 0.000 ARG A 702 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1814.35 seconds wall clock time: 33 minutes 46.29 seconds (2026.29 seconds total)