Starting phenix.real_space_refine on Fri May 9 13:06:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jmt_36426/05_2025/8jmt_36426_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jmt_36426/05_2025/8jmt_36426.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jmt_36426/05_2025/8jmt_36426.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jmt_36426/05_2025/8jmt_36426.map" model { file = "/net/cci-nas-00/data/ceres_data/8jmt_36426/05_2025/8jmt_36426_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jmt_36426/05_2025/8jmt_36426_neut.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.054 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: 4 Type Number sf(0) Gaussians S 17 5.16 5 C 1284 2.51 5 N 296 2.21 5 O 297 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 1894 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1894 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 3, 'TRANS': 230} Chain breaks: 3 Time building chain proxies: 2.05, per 1000 atoms: 1.08 Number of scatterers: 1894 At special positions: 0 Unit cell: (63.13, 67.41, 65.27, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 17 16.00 O 297 8.00 N 296 7.00 C 1284 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 882 " - pdb=" SG CYS A1201 " distance=2.03 Simple disulfide: pdb=" SG CYS A 927 " - pdb=" SG CYS A 999 " distance=2.03 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: 0.45 Conformation dependent library (CDL) restraints added in 218.2 milliseconds 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 442 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 0 sheets defined 81.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 861 through 882 removed outlier: 3.957A pdb=" N ILE A 867 " --> pdb=" O LEU A 863 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL A 870 " --> pdb=" O VAL A 866 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N CYS A 882 " --> pdb=" O CYS A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 917 removed outlier: 3.880A pdb=" N ILE A 899 " --> pdb=" O ASP A 895 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N HIS A 900 " --> pdb=" O ARG A 896 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N CYS A 904 " --> pdb=" O HIS A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 958 removed outlier: 3.763A pdb=" N LEU A 939 " --> pdb=" O HIS A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 988 removed outlier: 3.645A pdb=" N MET A 977 " --> pdb=" O VAL A 973 " (cutoff:3.500A) Proline residue: A 978 - end of helix Processing helix chain 'A' and resid 1007 through 1036 Proline residue: A1014 - end of helix Processing helix chain 'A' and resid 1148 through 1168 Processing helix chain 'A' and resid 1181 through 1200 removed outlier: 3.751A pdb=" N THR A1186 " --> pdb=" O ALA A1182 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE A1187 " --> pdb=" O TYR A1183 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N HIS A1200 " --> pdb=" O ILE A1196 " (cutoff:3.500A) Processing helix chain 'A' and resid 1206 through 1219 141 hydrogen bonds defined for protein. 423 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: 0.45 Time building geometry restraints manager: 0.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 545 1.34 - 1.46: 473 1.46 - 1.58: 900 1.58 - 1.70: 0 1.70 - 1.82: 25 Bond restraints: 1943 Sorted by residual: bond pdb=" CG LEU A1021 " pdb=" CD2 LEU A1021 " ideal model delta sigma weight residual 1.521 1.478 0.043 3.30e-02 9.18e+02 1.73e+00 bond pdb=" CA MET A 955 " pdb=" C MET A 955 " ideal model delta sigma weight residual 1.522 1.504 0.018 1.72e-02 3.38e+03 1.08e+00 bond pdb=" CA LEU A1021 " pdb=" C LEU A1021 " ideal model delta sigma weight residual 1.523 1.533 -0.010 1.37e-02 5.33e+03 5.85e-01 bond pdb=" N PHE A1025 " pdb=" CA PHE A1025 " ideal model delta sigma weight residual 1.459 1.468 -0.009 1.21e-02 6.83e+03 5.72e-01 bond pdb=" CA LYS A 901 " pdb=" C LYS A 901 " ideal model delta sigma weight residual 1.525 1.516 0.009 1.29e-02 6.01e+03 4.64e-01 ... (remaining 1938 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 2536 1.79 - 3.58: 88 3.58 - 5.37: 6 5.37 - 7.16: 0 7.16 - 8.95: 3 Bond angle restraints: 2633 Sorted by residual: angle pdb=" N VAL A1179 " pdb=" CA VAL A1179 " pdb=" C VAL A1179 " ideal model delta sigma weight residual 113.00 109.13 3.87 1.30e+00 5.92e-01 8.88e+00 angle pdb=" N LYS A1206 " pdb=" CA LYS A1206 " pdb=" C LYS A1206 " ideal model delta sigma weight residual 113.43 110.03 3.40 1.26e+00 6.30e-01 7.28e+00 angle pdb=" N CYS A 887 " pdb=" CA CYS A 887 " pdb=" C CYS A 887 " ideal model delta sigma weight residual 114.56 111.15 3.41 1.27e+00 6.20e-01 7.19e+00 angle pdb=" CA LEU A1021 " pdb=" CB LEU A1021 " pdb=" CG LEU A1021 " ideal model delta sigma weight residual 116.30 125.25 -8.95 3.50e+00 8.16e-02 6.54e+00 angle pdb=" CA SER A1177 " pdb=" C SER A1177 " pdb=" O SER A1177 " ideal model delta sigma weight residual 121.32 118.53 2.79 1.16e+00 7.43e-01 5.79e+00 ... (remaining 2628 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 986 17.92 - 35.84: 100 35.84 - 53.76: 19 53.76 - 71.68: 1 71.68 - 89.60: 2 Dihedral angle restraints: 1108 sinusoidal: 427 harmonic: 681 Sorted by residual: dihedral pdb=" CB CYS A 927 " pdb=" SG CYS A 927 " pdb=" SG CYS A 999 " pdb=" CB CYS A 999 " ideal model delta sinusoidal sigma weight residual -86.00 -127.16 41.16 1 1.00e+01 1.00e-02 2.37e+01 dihedral pdb=" CA TRP A1167 " pdb=" C TRP A1167 " pdb=" N ALA A1168 " pdb=" CA ALA A1168 " ideal model delta harmonic sigma weight residual 180.00 159.73 20.27 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA CYS A 882 " pdb=" C CYS A 882 " pdb=" N ILE A 883 " pdb=" CA ILE A 883 " ideal model delta harmonic sigma weight residual 180.00 160.31 19.69 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 1105 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 155 0.024 - 0.048: 77 0.048 - 0.072: 57 0.072 - 0.096: 15 0.096 - 0.119: 8 Chirality restraints: 312 Sorted by residual: chirality pdb=" CG LEU A1021 " pdb=" CB LEU A1021 " pdb=" CD1 LEU A1021 " pdb=" CD2 LEU A1021 " both_signs ideal model delta sigma weight residual False -2.59 -2.71 0.12 2.00e-01 2.50e+01 3.57e-01 chirality pdb=" CA MET A 945 " pdb=" N MET A 945 " pdb=" C MET A 945 " pdb=" CB MET A 945 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.52e-01 chirality pdb=" CA PHE A1007 " pdb=" N PHE A1007 " pdb=" C PHE A1007 " pdb=" CB PHE A1007 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 3.29e-01 ... (remaining 309 not shown) Planarity restraints: 308 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 977 " -0.022 5.00e-02 4.00e+02 3.37e-02 1.82e+00 pdb=" N PRO A 978 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 978 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 978 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A1164 " 0.006 2.00e-02 2.50e+03 1.21e-02 1.46e+00 pdb=" C GLY A1164 " -0.021 2.00e-02 2.50e+03 pdb=" O GLY A1164 " 0.008 2.00e-02 2.50e+03 pdb=" N LEU A1165 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A1025 " 0.009 2.00e-02 2.50e+03 8.72e-03 1.33e+00 pdb=" CG PHE A1025 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE A1025 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE A1025 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A1025 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A1025 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A1025 " 0.001 2.00e-02 2.50e+03 ... (remaining 305 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 148 2.74 - 3.28: 2002 3.28 - 3.82: 3149 3.82 - 4.36: 3605 4.36 - 4.90: 6170 Nonbonded interactions: 15074 Sorted by model distance: nonbonded pdb=" O PHE A1185 " pdb=" ND2 ASN A1189 " model vdw 2.204 3.120 nonbonded pdb=" O TYR A1031 " pdb=" ND1 HIS A1035 " model vdw 2.302 3.120 nonbonded pdb=" O PHE A 884 " pdb=" N PHE A 888 " model vdw 2.346 3.120 nonbonded pdb=" OG SER A 875 " pdb=" O ASN A1189 " model vdw 2.385 3.040 nonbonded pdb=" O ASP A1004 " pdb=" OG1 THR A1005 " model vdw 2.478 3.040 ... (remaining 15069 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: 0.750 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 10.100 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:2.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5677 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 : 0.003 0.043 1945 Z= 0.154 Angle : 0.745 8.952 2637 Z= 0.455 Chirality : 0.040 0.119 312 Planarity : 0.004 0.034 308 Dihedral : 14.381 89.604 660 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.55), residues: 226 helix: 0.64 (0.37), residues: 184 sheet: None (None), residues: 0 loop : -2.71 (0.92), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 944 HIS 0.003 0.001 HIS A 935 PHE 0.020 0.002 PHE A1025 TYR 0.005 0.001 TYR A 969 ARG 0.002 0.000 ARG A 920 Details of bonding type rmsd hydrogen bonds : bond 0.14957 ( 141) hydrogen bonds : angle 6.10822 ( 423) SS BOND : bond 0.00193 ( 2) SS BOND : angle 0.94172 ( 4) covalent geometry : bond 0.00301 ( 1943) covalent geometry : angle 0.74489 ( 2633) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.185 Fit side-chains REVERT: A 1194 MET cc_start: 0.6675 (tpp) cc_final: 0.5731 (tpt) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0820 time to fit residues: 2.0488 Evaluate side-chains 16 residues out of total 203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 19 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 11 optimal weight: 0.0570 chunk 18 optimal weight: 0.9980 chunk 6 optimal weight: 0.0670 chunk 10 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 900 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1204 GLN ** 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 = 0.4675 r_free = 0.4675 target = 0.259341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.220639 restraints weight = 2230.359| |-----------------------------------------------------------------------------| r_work (start): 0.4263 rms_B_bonded: 2.27 r_work: 0.4138 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.4138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5635 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 1945 Z= 0.142 Angle : 0.589 6.020 2637 Z= 0.304 Chirality : 0.041 0.113 312 Planarity : 0.004 0.028 308 Dihedral : 4.571 21.106 247 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.55), residues: 226 helix: 1.04 (0.37), residues: 188 sheet: None (None), residues: 0 loop : -2.88 (0.94), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 944 HIS 0.003 0.001 HIS A 900 PHE 0.012 0.002 PHE A1199 TYR 0.006 0.001 TYR A1031 ARG 0.001 0.000 ARG A 967 Details of bonding type rmsd hydrogen bonds : bond 0.03745 ( 141) hydrogen bonds : angle 4.09909 ( 423) SS BOND : bond 0.00167 ( 2) SS BOND : angle 1.09048 ( 4) covalent geometry : bond 0.00332 ( 1943) covalent geometry : angle 0.58757 ( 2633) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.180 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0936 time to fit residues: 2.2046 Evaluate side-chains 16 residues out of total 203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 4 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 11 optimal weight: 0.0370 chunk 10 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 3 optimal weight: 0.0980 chunk 14 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 overall best weight: 0.3858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 897 ASN ** A1192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1204 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4708 r_free = 0.4708 target = 0.261682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.222773 restraints weight = 2208.439| |-----------------------------------------------------------------------------| r_work (start): 0.4255 rms_B_bonded: 2.23 r_work: 0.4128 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.4128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5655 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 1945 Z= 0.129 Angle : 0.535 4.977 2637 Z= 0.283 Chirality : 0.040 0.109 312 Planarity : 0.003 0.029 308 Dihedral : 4.387 20.775 247 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.00 % Allowed : 11.82 % Favored : 88.18 % 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: 1.17 (0.55), residues: 226 helix: 1.41 (0.37), residues: 185 sheet: None (None), residues: 0 loop : -2.13 (0.98), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 944 HIS 0.003 0.001 HIS A1035 PHE 0.012 0.002 PHE A 888 TYR 0.005 0.001 TYR A1031 ARG 0.001 0.000 ARG A 896 Details of bonding type rmsd hydrogen bonds : bond 0.03507 ( 141) hydrogen bonds : angle 3.90690 ( 423) SS BOND : bond 0.00201 ( 2) SS BOND : angle 1.01031 ( 4) covalent geometry : bond 0.00302 ( 1943) covalent geometry : angle 0.53388 ( 2633) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.210 Fit side-chains REVERT: A 1001 LEU cc_start: 0.6391 (tp) cc_final: 0.6059 (tp) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0955 time to fit residues: 2.3694 Evaluate side-chains 16 residues out of total 203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 15 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 22 optimal weight: 0.4980 chunk 7 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 900 HIS ** 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 = 0.4626 r_free = 0.4626 target = 0.252995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.215430 restraints weight = 2132.656| |-----------------------------------------------------------------------------| r_work (start): 0.4220 rms_B_bonded: 2.08 r_work: 0.4097 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.4097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5756 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 1945 Z= 0.168 Angle : 0.593 5.958 2637 Z= 0.310 Chirality : 0.042 0.142 312 Planarity : 0.004 0.032 308 Dihedral : 4.637 23.263 247 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.48 % Allowed : 14.29 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.55), residues: 226 helix: 1.17 (0.36), residues: 188 sheet: None (None), residues: 0 loop : -2.50 (0.98), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 944 HIS 0.003 0.001 HIS A1036 PHE 0.014 0.002 PHE A1195 TYR 0.007 0.001 TYR A1031 ARG 0.002 0.000 ARG A 967 Details of bonding type rmsd hydrogen bonds : bond 0.03909 ( 141) hydrogen bonds : angle 4.03737 ( 423) SS BOND : bond 0.00189 ( 2) SS BOND : angle 1.25201 ( 4) covalent geometry : bond 0.00405 ( 1943) covalent geometry : angle 0.59157 ( 2633) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 18 time to evaluate : 0.193 Fit side-chains REVERT: A 945 MET cc_start: 0.7239 (mtp) cc_final: 0.6810 (ttp) REVERT: A 955 MET cc_start: 0.7054 (mtp) cc_final: 0.6669 (mtp) REVERT: A 977 MET cc_start: 0.3696 (tpp) cc_final: 0.3440 (ttm) REVERT: A 1001 LEU cc_start: 0.6582 (tp) cc_final: 0.6111 (tp) outliers start: 3 outliers final: 2 residues processed: 20 average time/residue: 0.0907 time to fit residues: 2.4515 Evaluate side-chains 20 residues out of total 203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 18 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1033 MET Chi-restraints excluded: chain A residue 1035 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 12 optimal weight: 0.0070 chunk 9 optimal weight: 0.4980 chunk 8 optimal weight: 0.5980 chunk 2 optimal weight: 0.0270 chunk 14 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 22 optimal weight: 0.0770 chunk 6 optimal weight: 0.8980 chunk 16 optimal weight: 0.1980 chunk 18 optimal weight: 0.9990 overall best weight: 0.1614 ------------------------------------------------------------------------------- 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 = 0.4683 r_free = 0.4683 target = 0.260304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.221064 restraints weight = 2164.456| |-----------------------------------------------------------------------------| r_work (start): 0.4265 rms_B_bonded: 2.29 r_work: 0.4140 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.4140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5605 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 1945 Z= 0.100 Angle : 0.480 4.907 2637 Z= 0.254 Chirality : 0.038 0.115 312 Planarity : 0.003 0.031 308 Dihedral : 4.059 19.200 247 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.49 % Allowed : 16.75 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.56), residues: 226 helix: 1.70 (0.37), residues: 188 sheet: None (None), residues: 0 loop : -2.16 (1.03), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 944 HIS 0.002 0.001 HIS A 935 PHE 0.010 0.001 PHE A 937 TYR 0.005 0.001 TYR A 971 ARG 0.001 0.000 ARG A 920 Details of bonding type rmsd hydrogen bonds : bond 0.03062 ( 141) hydrogen bonds : angle 3.65087 ( 423) SS BOND : bond 0.00212 ( 2) SS BOND : angle 0.72978 ( 4) covalent geometry : bond 0.00224 ( 1943) covalent geometry : angle 0.47946 ( 2633) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 19 time to evaluate : 0.180 Fit side-chains REVERT: A 1021 LEU cc_start: 0.3707 (OUTLIER) cc_final: 0.3137 (tt) outliers start: 1 outliers final: 0 residues processed: 20 average time/residue: 0.0917 time to fit residues: 2.4569 Evaluate side-chains 18 residues out of total 203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 17 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1021 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 20 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 22 optimal weight: 0.2980 chunk 2 optimal weight: 0.0060 chunk 10 optimal weight: 0.4980 chunk 3 optimal weight: 0.0980 chunk 13 optimal weight: 0.7980 chunk 4 optimal weight: 0.3980 chunk 21 optimal weight: 0.8980 chunk 8 optimal weight: 0.3980 overall best weight: 0.2396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1022 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 = 0.4583 r_free = 0.4583 target = 0.251603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.210236 restraints weight = 2136.501| |-----------------------------------------------------------------------------| r_work (start): 0.4264 rms_B_bonded: 2.27 r_work: 0.4136 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.4136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5657 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 1945 Z= 0.108 Angle : 0.490 4.926 2637 Z= 0.258 Chirality : 0.038 0.098 312 Planarity : 0.003 0.030 308 Dihedral : 4.017 19.140 247 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.97 % Allowed : 16.75 % Favored : 81.28 % 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: 1.85 (0.55), residues: 226 helix: 1.93 (0.37), residues: 186 sheet: None (None), residues: 0 loop : -2.23 (0.90), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 944 HIS 0.002 0.001 HIS A1036 PHE 0.011 0.001 PHE A1185 TYR 0.006 0.001 TYR A 953 ARG 0.001 0.000 ARG A 967 Details of bonding type rmsd hydrogen bonds : bond 0.03143 ( 141) hydrogen bonds : angle 3.56385 ( 423) SS BOND : bond 0.00165 ( 2) SS BOND : angle 0.78287 ( 4) covalent geometry : bond 0.00250 ( 1943) covalent geometry : angle 0.48981 ( 2633) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 17 time to evaluate : 0.192 Fit side-chains REVERT: A 945 MET cc_start: 0.7556 (ttm) cc_final: 0.7110 (tpp) REVERT: A 1021 LEU cc_start: 0.3682 (OUTLIER) cc_final: 0.3065 (tt) REVERT: A 1196 ILE cc_start: 0.4561 (OUTLIER) cc_final: 0.4271 (mm) outliers start: 4 outliers final: 2 residues processed: 20 average time/residue: 0.0875 time to fit residues: 2.3930 Evaluate side-chains 21 residues out of total 203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 17 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 918 ILE Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1196 ILE Chi-restraints excluded: chain A residue 1202 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 10 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1022 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 = 0.4516 r_free = 0.4516 target = 0.242652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.206274 restraints weight = 2103.144| |-----------------------------------------------------------------------------| r_work (start): 0.4243 rms_B_bonded: 2.25 r_work: 0.4065 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.4065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5880 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 1945 Z= 0.173 Angle : 0.602 7.040 2637 Z= 0.312 Chirality : 0.043 0.150 312 Planarity : 0.003 0.031 308 Dihedral : 4.526 23.166 247 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.96 % Allowed : 16.75 % Favored : 80.30 % 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: 1.31 (0.54), residues: 226 helix: 1.55 (0.36), residues: 186 sheet: None (None), residues: 0 loop : -2.38 (0.90), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 944 HIS 0.003 0.001 HIS A1036 PHE 0.015 0.002 PHE A 888 TYR 0.010 0.002 TYR A 953 ARG 0.003 0.001 ARG A 896 Details of bonding type rmsd hydrogen bonds : bond 0.03978 ( 141) hydrogen bonds : angle 3.91570 ( 423) SS BOND : bond 0.00239 ( 2) SS BOND : angle 1.24252 ( 4) covalent geometry : bond 0.00418 ( 1943) covalent geometry : angle 0.60057 ( 2633) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 18 time to evaluate : 0.189 Fit side-chains REVERT: A 945 MET cc_start: 0.7712 (ttm) cc_final: 0.7373 (tpp) REVERT: A 1001 LEU cc_start: 0.6838 (tp) cc_final: 0.6373 (tp) REVERT: A 1021 LEU cc_start: 0.3672 (OUTLIER) cc_final: 0.3050 (tt) outliers start: 6 outliers final: 4 residues processed: 23 average time/residue: 0.0870 time to fit residues: 2.6846 Evaluate side-chains 23 residues out of total 203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 18 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 918 ILE Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1033 MET Chi-restraints excluded: chain A residue 1035 HIS Chi-restraints excluded: chain A residue 1202 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 22 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 3 optimal weight: 0.0470 chunk 17 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 21 optimal weight: 0.1980 chunk 11 optimal weight: 0.4980 chunk 2 optimal weight: 0.0670 chunk 19 optimal weight: 2.9990 chunk 12 optimal weight: 0.4980 overall best weight: 0.2616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1022 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 = 0.4570 r_free = 0.4570 target = 0.249363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.212476 restraints weight = 2191.281| |-----------------------------------------------------------------------------| r_work (start): 0.4292 rms_B_bonded: 2.42 r_work: 0.4122 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.4122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5714 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 1945 Z= 0.111 Angle : 0.499 4.928 2637 Z= 0.262 Chirality : 0.039 0.116 312 Planarity : 0.003 0.029 308 Dihedral : 4.072 19.908 247 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.46 % Allowed : 17.73 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.55), residues: 226 helix: 1.88 (0.36), residues: 186 sheet: None (None), residues: 0 loop : -2.31 (0.88), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 944 HIS 0.002 0.001 HIS A 935 PHE 0.012 0.001 PHE A1185 TYR 0.006 0.001 TYR A 953 ARG 0.001 0.000 ARG A 967 Details of bonding type rmsd hydrogen bonds : bond 0.03326 ( 141) hydrogen bonds : angle 3.68234 ( 423) SS BOND : bond 0.00186 ( 2) SS BOND : angle 0.87814 ( 4) covalent geometry : bond 0.00257 ( 1943) covalent geometry : angle 0.49813 ( 2633) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 17 time to evaluate : 0.205 Fit side-chains revert: symmetry clash REVERT: A 923 GLN cc_start: 0.5984 (mm110) cc_final: 0.5772 (mm110) REVERT: A 945 MET cc_start: 0.7527 (ttm) cc_final: 0.7155 (tpp) REVERT: A 1021 LEU cc_start: 0.3582 (OUTLIER) cc_final: 0.3010 (tt) outliers start: 5 outliers final: 4 residues processed: 22 average time/residue: 0.0988 time to fit residues: 2.8845 Evaluate side-chains 21 residues out of total 203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 16 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 918 ILE Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1035 HIS Chi-restraints excluded: chain A residue 1036 HIS Chi-restraints excluded: chain A residue 1202 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 8 optimal weight: 0.3980 chunk 4 optimal weight: 0.5980 chunk 11 optimal weight: 0.0270 chunk 19 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 16 optimal weight: 0.3980 chunk 7 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.4038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1022 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 = 0.4560 r_free = 0.4560 target = 0.247123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.206324 restraints weight = 2238.906| |-----------------------------------------------------------------------------| r_work (start): 0.4205 rms_B_bonded: 2.38 r_work: 0.4078 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.4078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5712 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 1945 Z= 0.132 Angle : 0.533 5.149 2637 Z= 0.277 Chirality : 0.040 0.123 312 Planarity : 0.003 0.030 308 Dihedral : 4.188 20.910 247 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.46 % Allowed : 17.73 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.54), residues: 226 helix: 1.86 (0.36), residues: 186 sheet: None (None), residues: 0 loop : -2.28 (0.88), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 944 HIS 0.002 0.001 HIS A1036 PHE 0.011 0.001 PHE A 888 TYR 0.008 0.001 TYR A 953 ARG 0.002 0.000 ARG A 896 Details of bonding type rmsd hydrogen bonds : bond 0.03499 ( 141) hydrogen bonds : angle 3.72068 ( 423) SS BOND : bond 0.00183 ( 2) SS BOND : angle 0.98572 ( 4) covalent geometry : bond 0.00314 ( 1943) covalent geometry : angle 0.53187 ( 2633) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 17 time to evaluate : 0.197 Fit side-chains revert: symmetry clash REVERT: A 945 MET cc_start: 0.7559 (ttm) cc_final: 0.7249 (tpp) REVERT: A 1021 LEU cc_start: 0.3510 (OUTLIER) cc_final: 0.2934 (tt) outliers start: 5 outliers final: 4 residues processed: 22 average time/residue: 0.0962 time to fit residues: 2.7902 Evaluate side-chains 22 residues out of total 203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 17 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 918 ILE Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1035 HIS Chi-restraints excluded: chain A residue 1036 HIS Chi-restraints excluded: chain A residue 1202 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 10 optimal weight: 0.6980 chunk 13 optimal weight: 0.0000 chunk 22 optimal weight: 0.0970 chunk 4 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 2 optimal weight: 0.4980 chunk 6 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 overall best weight: 0.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1022 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 = 0.4562 r_free = 0.4562 target = 0.248035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.208262 restraints weight = 2163.128| |-----------------------------------------------------------------------------| r_work (start): 0.4234 rms_B_bonded: 2.24 r_work: 0.4102 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.4102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5753 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 1945 Z= 0.124 Angle : 0.523 5.153 2637 Z= 0.272 Chirality : 0.040 0.128 312 Planarity : 0.003 0.030 308 Dihedral : 4.116 20.232 247 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.46 % Allowed : 17.73 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.54), residues: 226 helix: 1.95 (0.36), residues: 186 sheet: None (None), residues: 0 loop : -2.35 (0.85), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 944 HIS 0.002 0.001 HIS A1036 PHE 0.011 0.001 PHE A1185 TYR 0.006 0.001 TYR A 953 ARG 0.002 0.000 ARG A 896 Details of bonding type rmsd hydrogen bonds : bond 0.03392 ( 141) hydrogen bonds : angle 3.67873 ( 423) SS BOND : bond 0.00177 ( 2) SS BOND : angle 0.90985 ( 4) covalent geometry : bond 0.00293 ( 1943) covalent geometry : angle 0.52262 ( 2633) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 18 time to evaluate : 0.196 Fit side-chains revert: symmetry clash REVERT: A 945 MET cc_start: 0.7601 (ttm) cc_final: 0.7282 (tpp) REVERT: A 1001 LEU cc_start: 0.6806 (tp) cc_final: 0.6397 (tp) REVERT: A 1021 LEU cc_start: 0.3657 (OUTLIER) cc_final: 0.3080 (tt) outliers start: 5 outliers final: 3 residues processed: 23 average time/residue: 0.0900 time to fit residues: 2.7539 Evaluate side-chains 21 residues out of total 203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 17 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1035 HIS Chi-restraints excluded: chain A residue 1036 HIS Chi-restraints excluded: chain A residue 1202 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 15 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 16 optimal weight: 0.2980 chunk 21 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 6 optimal weight: 0.3980 chunk 10 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1022 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 = 0.4527 r_free = 0.4527 target = 0.243883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.207821 restraints weight = 2173.792| |-----------------------------------------------------------------------------| r_work (start): 0.4252 rms_B_bonded: 2.32 r_work: 0.4074 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.4074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5785 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 1945 Z= 0.152 Angle : 0.577 6.039 2637 Z= 0.298 Chirality : 0.041 0.126 312 Planarity : 0.003 0.029 308 Dihedral : 4.392 21.927 247 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.97 % Allowed : 17.73 % Favored : 80.30 % 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: 1.62 (0.54), residues: 226 helix: 1.77 (0.36), residues: 186 sheet: None (None), residues: 0 loop : -2.35 (0.86), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 944 HIS 0.003 0.001 HIS A1036 PHE 0.013 0.002 PHE A 888 TYR 0.009 0.001 TYR A 953 ARG 0.003 0.000 ARG A 896 Details of bonding type rmsd hydrogen bonds : bond 0.03731 ( 141) hydrogen bonds : angle 3.82034 ( 423) SS BOND : bond 0.00210 ( 2) SS BOND : angle 1.10767 ( 4) covalent geometry : bond 0.00364 ( 1943) covalent geometry : angle 0.57591 ( 2633) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1523.34 seconds wall clock time: 27 minutes 12.01 seconds (1632.01 seconds total)