Starting phenix.real_space_refine on Wed Feb 12 10:16:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tqm_41508/02_2025/8tqm_41508_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tqm_41508/02_2025/8tqm_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/cci-nas-00/data/ceres_data/8tqm_41508/02_2025/8tqm_41508.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tqm_41508/02_2025/8tqm_41508.map" model { file = "/net/cci-nas-00/data/ceres_data/8tqm_41508/02_2025/8tqm_41508_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tqm_41508/02_2025/8tqm_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 Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 5.15, per 1000 atoms: 0.71 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.44 Conformation dependent library (CDL) restraints added in 787.6 milliseconds 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: 0.71 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: 2.11 Time building geometry restraints manager: 2.59 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: 0.00 - 4.20: 9939 4.20 - 8.41: 72 8.41 - 12.61: 9 12.61 - 16.82: 2 16.82 - 21.02: 1 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 3.040 nonbonded pdb=" ND2 ASN A 699 " pdb=" OE2 GLU A 808 " model vdw 2.212 3.120 nonbonded pdb=" NE2 HIS A 213 " pdb=" O1 ERG A1407 " model vdw 2.264 3.120 ... (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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.280 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: 0.060 Set scattering table: 0.060 Process input model: 20.660 Find NCS groups from input model: 0.060 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:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.530 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.748 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: 0.2190 time to fit residues: 38.9022 Evaluate side-chains 92 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.746 ------------------------------------------------------------------------------- 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: 0.9990 chunk 63 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 65 optimal weight: 0.0470 chunk 25 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- 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 ** A1181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.193826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.140451 restraints weight = 7748.748| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 2.67 r_work: 0.3047 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.1574 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 : 0.554 8.118 10023 Z= 0.281 Chirality : 0.039 0.159 1123 Planarity : 0.004 0.052 1170 Dihedral : 12.632 75.166 1278 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.26 % Allowed : 7.07 % Favored : 92.67 % 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: 2.35 (0.29), residues: 831 helix: 2.21 (0.20), residues: 661 sheet: -1.55 (1.08), residues: 22 loop : -1.02 (0.51), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 149 HIS 0.003 0.001 HIS A 721 PHE 0.016 0.001 PHE A 614 TYR 0.029 0.001 TYR A 965 ARG 0.004 0.000 ARG A 702 *********************** 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 100 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 98 time to evaluate : 0.814 Fit side-chains REVERT: A 599 TYR cc_start: 0.8098 (m-80) cc_final: 0.7755 (m-80) REVERT: A 816 LYS cc_start: 0.8599 (tttt) cc_final: 0.7788 (mttm) REVERT: A 835 THR cc_start: 0.9171 (t) cc_final: 0.8794 (m) REVERT: A 1047 ILE cc_start: 0.7055 (mt) cc_final: 0.6807 (mt) outliers start: 2 outliers final: 1 residues processed: 100 average time/residue: 0.2048 time to fit residues: 27.9356 Evaluate side-chains 90 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 89 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 70 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 80 optimal weight: 8.9990 chunk 71 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 31 optimal weight: 0.0070 chunk 73 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 overall best weight: 0.7400 ------------------------------------------------------------------------------- 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** ** A1181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.192285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.140114 restraints weight = 7789.525| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.91 r_work: 0.2938 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7423 Z= 0.231 Angle : 0.539 7.725 10023 Z= 0.273 Chirality : 0.039 0.145 1123 Planarity : 0.004 0.053 1170 Dihedral : 12.348 80.765 1278 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.65 % Allowed : 9.29 % Favored : 90.05 % 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: 2.26 (0.29), residues: 831 helix: 2.15 (0.20), residues: 662 sheet: -1.63 (1.10), residues: 22 loop : -1.04 (0.50), residues: 147 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 0.015 0.001 PHE A 614 TYR 0.026 0.001 TYR A 965 ARG 0.005 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 99 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 94 time to evaluate : 0.791 Fit side-chains REVERT: A 172 LYS cc_start: 0.7959 (ttmt) cc_final: 0.7434 (ttmm) REVERT: A 175 ILE cc_start: 0.8643 (mm) cc_final: 0.8213 (mt) REVERT: A 710 ARG cc_start: 0.7593 (ttm170) cc_final: 0.7091 (ttm-80) REVERT: A 816 LYS cc_start: 0.8635 (tttt) cc_final: 0.7826 (mttm) REVERT: A 835 THR cc_start: 0.9107 (t) cc_final: 0.8725 (m) REVERT: A 1047 ILE cc_start: 0.7040 (mt) cc_final: 0.6792 (mt) REVERT: A 1106 ASP cc_start: 0.7507 (m-30) cc_final: 0.6839 (m-30) outliers start: 5 outliers final: 2 residues processed: 97 average time/residue: 0.1891 time to fit residues: 25.3429 Evaluate side-chains 87 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 85 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 477 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 26 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 18 optimal weight: 20.0000 chunk 25 optimal weight: 0.3980 chunk 15 optimal weight: 0.9990 chunk 37 optimal weight: 0.0270 chunk 3 optimal weight: 0.9980 overall best weight: 0.5438 ------------------------------------------------------------------------------- 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** ** A1181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.195623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.148847 restraints weight = 7741.778| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 2.85 r_work: 0.2988 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.2250 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= 0.187 Angle : 0.500 7.170 10023 Z= 0.256 Chirality : 0.037 0.139 1123 Planarity : 0.004 0.055 1170 Dihedral : 12.044 81.877 1278 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.92 % Allowed : 10.60 % Favored : 88.48 % 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: 2.41 (0.29), residues: 831 helix: 2.24 (0.20), residues: 662 sheet: -1.47 (1.13), residues: 22 loop : -0.93 (0.51), residues: 147 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 0.023 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 94 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 0.720 Fit side-chains revert: symmetry clash REVERT: A 175 ILE cc_start: 0.8717 (mm) cc_final: 0.8299 (mt) REVERT: A 710 ARG cc_start: 0.7517 (ttm170) cc_final: 0.7084 (ttm-80) REVERT: A 816 LYS cc_start: 0.8615 (tttt) cc_final: 0.7808 (mttm) REVERT: A 1015 VAL cc_start: 0.7883 (t) cc_final: 0.7446 (m) REVERT: A 1047 ILE cc_start: 0.6966 (mt) cc_final: 0.6690 (mt) outliers start: 7 outliers final: 3 residues processed: 89 average time/residue: 0.1654 time to fit residues: 21.0677 Evaluate side-chains 89 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 86 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 195 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 71 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 19 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 6 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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** A1181 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.190280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.137992 restraints weight = 7665.846| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.93 r_work: 0.3018 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 7423 Z= 0.304 Angle : 0.559 7.669 10023 Z= 0.282 Chirality : 0.040 0.151 1123 Planarity : 0.004 0.053 1170 Dihedral : 12.513 79.594 1278 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.44 % Allowed : 11.13 % Favored : 87.43 % 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: 2.13 (0.29), residues: 831 helix: 2.06 (0.20), residues: 662 sheet: -1.79 (1.06), residues: 22 loop : -1.09 (0.50), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 662 HIS 0.007 0.001 HIS A 721 PHE 0.013 0.001 PHE A 614 TYR 0.026 0.001 TYR A 965 ARG 0.003 0.000 ARG A 964 *********************** 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 99 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.822 Fit side-chains REVERT: A 175 ILE cc_start: 0.8742 (mm) cc_final: 0.8370 (mt) REVERT: A 1106 ASP cc_start: 0.7478 (m-30) cc_final: 0.6797 (m-30) outliers start: 11 outliers final: 5 residues processed: 94 average time/residue: 0.1567 time to fit residues: 21.4985 Evaluate side-chains 88 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 83 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 1029 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 12 optimal weight: 0.3980 chunk 77 optimal weight: 4.9990 chunk 60 optimal weight: 0.5980 chunk 83 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 1 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.190861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.141579 restraints weight = 7764.317| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 3.11 r_work: 0.2896 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.2578 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= 0.207 Angle : 0.502 7.162 10023 Z= 0.258 Chirality : 0.038 0.140 1123 Planarity : 0.004 0.056 1170 Dihedral : 12.218 80.988 1278 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.52 % Allowed : 12.43 % Favored : 87.04 % 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: 2.26 (0.29), residues: 831 helix: 2.16 (0.20), residues: 663 sheet: -1.79 (1.07), residues: 22 loop : -1.09 (0.50), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 662 HIS 0.003 0.001 HIS A 839 PHE 0.012 0.001 PHE A 614 TYR 0.022 0.001 TYR A 965 ARG 0.002 0.000 ARG A 225 *********************** 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 87 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 83 time to evaluate : 0.726 Fit side-chains REVERT: A 175 ILE cc_start: 0.8735 (mm) cc_final: 0.8362 (mt) REVERT: A 1106 ASP cc_start: 0.7473 (m-30) cc_final: 0.6795 (m-30) REVERT: A 1266 MET cc_start: 0.5119 (ppp) cc_final: 0.4713 (ppp) outliers start: 4 outliers final: 3 residues processed: 84 average time/residue: 0.1601 time to fit residues: 19.3230 Evaluate side-chains 86 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 83 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 695 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 47 optimal weight: 0.4980 chunk 28 optimal weight: 0.5980 chunk 61 optimal weight: 0.6980 chunk 56 optimal weight: 0.0030 chunk 12 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 50 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 932 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.191842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.140326 restraints weight = 7695.229| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 3.01 r_work: 0.2941 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7423 Z= 0.191 Angle : 0.497 7.051 10023 Z= 0.255 Chirality : 0.038 0.140 1123 Planarity : 0.004 0.055 1170 Dihedral : 11.995 81.904 1278 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.79 % Allowed : 12.57 % 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: 2.35 (0.29), residues: 831 helix: 2.22 (0.20), residues: 663 sheet: -1.88 (1.03), residues: 22 loop : -1.04 (0.51), residues: 146 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 0.022 0.001 TYR A 965 ARG 0.002 0.000 ARG A1126 *********************** 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 94 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 0.778 Fit side-chains REVERT: A 175 ILE cc_start: 0.8696 (mm) cc_final: 0.8326 (mt) REVERT: A 505 TYR cc_start: 0.8140 (m-10) cc_final: 0.7815 (m-10) REVERT: A 1106 ASP cc_start: 0.7456 (m-30) cc_final: 0.6829 (m-30) REVERT: A 1266 MET cc_start: 0.4974 (ppp) cc_final: 0.4610 (ppp) outliers start: 6 outliers final: 3 residues processed: 89 average time/residue: 0.1618 time to fit residues: 21.0080 Evaluate side-chains 87 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 84 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 695 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 69 optimal weight: 6.9990 chunk 81 optimal weight: 20.0000 chunk 76 optimal weight: 0.6980 chunk 55 optimal weight: 0.3980 chunk 28 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 54 optimal weight: 0.0570 chunk 71 optimal weight: 0.9980 chunk 31 optimal weight: 0.0970 chunk 65 optimal weight: 0.8980 overall best weight: 0.4296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 932 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.193708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.141863 restraints weight = 7832.992| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 2.71 r_work: 0.3105 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.2796 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= 0.165 Angle : 0.484 7.090 10023 Z= 0.251 Chirality : 0.037 0.138 1123 Planarity : 0.004 0.056 1170 Dihedral : 11.666 84.283 1278 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.79 % Allowed : 12.43 % Favored : 86.78 % 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: 663 sheet: -1.83 (1.05), residues: 22 loop : -1.00 (0.51), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 662 HIS 0.002 0.001 HIS A 721 PHE 0.012 0.001 PHE A1203 TYR 0.020 0.001 TYR A 965 ARG 0.002 0.000 ARG A 225 *********************** 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 94 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 0.720 Fit side-chains REVERT: A 175 ILE cc_start: 0.8713 (mm) cc_final: 0.8352 (mt) REVERT: A 505 TYR cc_start: 0.8137 (m-10) cc_final: 0.7841 (m-10) REVERT: A 816 LYS cc_start: 0.8538 (tttt) cc_final: 0.7758 (mttm) REVERT: A 1106 ASP cc_start: 0.7470 (m-30) cc_final: 0.6874 (m-30) REVERT: A 1266 MET cc_start: 0.5037 (ppp) cc_final: 0.4694 (ppp) outliers start: 6 outliers final: 4 residues processed: 90 average time/residue: 0.1762 time to fit residues: 22.7257 Evaluate side-chains 89 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 85 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 695 MET Chi-restraints excluded: chain A residue 1218 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 8 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 18 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 16 optimal weight: 0.0030 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 859 ASN A 932 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.192681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.141153 restraints weight = 7757.048| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.87 r_work: 0.2929 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.2931 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= 0.199 Angle : 0.500 6.420 10023 Z= 0.259 Chirality : 0.038 0.138 1123 Planarity : 0.004 0.055 1170 Dihedral : 11.690 89.052 1278 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.65 % Allowed : 13.22 % Favored : 86.13 % 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: 2.37 (0.29), residues: 831 helix: 2.23 (0.20), residues: 663 sheet: -1.79 (1.07), residues: 22 loop : -1.01 (0.51), residues: 146 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 A1126 *********************** 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 88 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 83 time to evaluate : 0.754 Fit side-chains REVERT: A 175 ILE cc_start: 0.8711 (mm) cc_final: 0.8356 (mt) REVERT: A 505 TYR cc_start: 0.8155 (m-10) cc_final: 0.7889 (m-10) REVERT: A 816 LYS cc_start: 0.8583 (tttt) cc_final: 0.7766 (mttm) REVERT: A 1266 MET cc_start: 0.5003 (ppp) cc_final: 0.4660 (ppp) outliers start: 5 outliers final: 5 residues processed: 84 average time/residue: 0.1763 time to fit residues: 21.3828 Evaluate side-chains 86 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 81 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 695 MET 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 59 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 80 optimal weight: 9.9990 chunk 45 optimal weight: 0.7980 chunk 3 optimal weight: 0.4980 chunk 12 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 932 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.190980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.140502 restraints weight = 7876.067| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 3.12 r_work: 0.2871 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 7423 Z= 0.294 Angle : 0.555 6.463 10023 Z= 0.283 Chirality : 0.040 0.185 1123 Planarity : 0.004 0.053 1170 Dihedral : 12.222 88.168 1278 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.79 % Allowed : 13.22 % Favored : 85.99 % 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: 2.14 (0.29), residues: 831 helix: 2.07 (0.20), residues: 663 sheet: -1.99 (1.05), residues: 22 loop : -1.09 (0.50), residues: 146 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 0.025 0.001 TYR A 965 ARG 0.003 0.000 ARG A 964 ********************** 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 91 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 0.731 Fit side-chains REVERT: A 175 ILE cc_start: 0.8740 (mm) cc_final: 0.8386 (mt) REVERT: A 505 TYR cc_start: 0.8250 (m-10) cc_final: 0.7962 (m-10) REVERT: A 710 ARG cc_start: 0.7725 (ttm110) cc_final: 0.7523 (ttm-80) REVERT: A 1266 MET cc_start: 0.5049 (ppp) cc_final: 0.4698 (ppp) outliers start: 6 outliers final: 5 residues processed: 87 average time/residue: 0.1738 time to fit residues: 22.1994 Evaluate side-chains 88 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 83 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 695 MET 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 76 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 19 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 46 optimal weight: 0.4980 chunk 52 optimal weight: 0.7980 chunk 78 optimal weight: 6.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 932 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.193514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.141613 restraints weight = 7724.153| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 3.04 r_work: 0.3058 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7423 Z= 0.212 Angle : 0.519 6.226 10023 Z= 0.268 Chirality : 0.038 0.141 1123 Planarity : 0.004 0.055 1170 Dihedral : 11.803 82.800 1278 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.65 % Allowed : 13.22 % Favored : 86.13 % 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: 2.29 (0.29), residues: 831 helix: 2.17 (0.20), residues: 662 sheet: -2.15 (0.99), residues: 22 loop : -0.93 (0.52), residues: 147 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 0.019 0.001 PHE A 999 TYR 0.023 0.001 TYR A 905 ARG 0.002 0.000 ARG A 964 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3953.25 seconds wall clock time: 70 minutes 49.68 seconds (4249.68 seconds total)