Starting phenix.real_space_refine on Sat Apr 26 15:23:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jmt_36426/04_2025/8jmt_36426_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jmt_36426/04_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_36426/04_2025/8jmt_36426.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jmt_36426/04_2025/8jmt_36426.map" model { file = "/net/cci-nas-00/data/ceres_data/8jmt_36426/04_2025/8jmt_36426_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jmt_36426/04_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-5669/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: 2.11, per 1000 atoms: 1.11 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: 0.50 Conformation dependent library (CDL) restraints added in 232.7 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: 0.17 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: 0.47 Time building geometry restraints manager: 0.56 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: 0.670 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: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.410 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.010 ------------------------------------------------------------------------------- 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: 0.0861 time to fit residues: 2.1633 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 : 0.188 ------------------------------------------------------------------------------- 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 = 57)----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.220621 restraints weight = 2230.359| |-----------------------------------------------------------------------------| r_work (start): 0.4262 rms_B_bonded: 2.27 r_work: 0.4136 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.4136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5630 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 : 0.188 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.1020 time to fit residues: 2.3937 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 : 0.202 ------------------------------------------------------------------------------- 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: 0.7980 chunk 10 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 3 optimal weight: 0.2980 chunk 14 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 897 ASN ** A 900 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4643 r_free = 0.4643 target = 0.254567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.215300 restraints weight = 2194.307| |-----------------------------------------------------------------------------| r_work (start): 0.4219 rms_B_bonded: 2.24 r_work: 0.4090 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.4090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5758 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 1945 Z= 0.164 Angle : 0.594 5.973 2637 Z= 0.313 Chirality : 0.042 0.144 312 Planarity : 0.004 0.032 308 Dihedral : 4.676 23.200 247 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.00 % Allowed : 10.84 % Favored : 89.16 % 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: 0.62 (0.55), residues: 226 helix: 1.07 (0.36), residues: 188 sheet: None (None), residues: 0 loop : -2.79 (0.95), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 944 HIS 0.004 0.002 HIS A1035 PHE 0.014 0.002 PHE A 888 TYR 0.008 0.001 TYR A1031 ARG 0.002 0.001 ARG A 896 Details of bonding type rmsd hydrogen bonds : bond 0.03908 ( 141) hydrogen bonds : angle 4.11314 ( 423) SS BOND : bond 0.00260 ( 2) SS BOND : angle 1.22834 ( 4) covalent geometry : bond 0.00392 ( 1943) covalent geometry : angle 0.59282 ( 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 17 residues out of total 203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.210 Fit side-chains REVERT: A 977 MET cc_start: 0.3794 (tpp) cc_final: 0.3500 (ttm) REVERT: A 1001 LEU cc_start: 0.6441 (tp) cc_final: 0.6073 (tp) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.1032 time to fit residues: 2.3897 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 : 0.201 ------------------------------------------------------------------------------- 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: 0.4980 chunk 3 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 12 optimal weight: 0.4980 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 = 0.4622 r_free = 0.4622 target = 0.252268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.212857 restraints weight = 2149.805| |-----------------------------------------------------------------------------| r_work (start): 0.4195 rms_B_bonded: 2.26 r_work: 0.4069 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.4069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5783 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 1945 Z= 0.166 Angle : 0.589 6.277 2637 Z= 0.310 Chirality : 0.042 0.144 312 Planarity : 0.004 0.034 308 Dihedral : 4.683 23.232 247 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.48 % Allowed : 13.30 % Favored : 85.22 % 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: 0.71 (0.55), residues: 226 helix: 1.11 (0.36), residues: 188 sheet: None (None), residues: 0 loop : -2.67 (0.96), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 944 HIS 0.003 0.001 HIS A1036 PHE 0.013 0.002 PHE A 884 TYR 0.008 0.001 TYR A1031 ARG 0.002 0.000 ARG A 967 Details of bonding type rmsd hydrogen bonds : bond 0.03814 ( 141) hydrogen bonds : angle 4.06270 ( 423) SS BOND : bond 0.00274 ( 2) SS BOND : angle 1.27531 ( 4) covalent geometry : bond 0.00399 ( 1943) covalent geometry : angle 0.58732 ( 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 20 residues out of total 203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 17 time to evaluate : 0.182 Fit side-chains REVERT: A 977 MET cc_start: 0.3687 (tpp) cc_final: 0.3449 (ttm) REVERT: A 1001 LEU cc_start: 0.6691 (tp) cc_final: 0.6185 (tp) outliers start: 3 outliers final: 1 residues processed: 19 average time/residue: 0.0944 time to fit residues: 2.4196 Evaluate side-chains 17 residues out of total 203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 16 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.5980 chunk 9 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 22 optimal weight: 0.4980 chunk 6 optimal weight: 0.0870 chunk 16 optimal weight: 0.3980 chunk 18 optimal weight: 1.9990 overall best weight: 0.4358 ------------------------------------------------------------------------------- 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 = 0.4637 r_free = 0.4637 target = 0.253840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.214229 restraints weight = 2185.355| |-----------------------------------------------------------------------------| r_work (start): 0.4208 rms_B_bonded: 2.29 r_work: 0.4081 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.4081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5734 moved from start: 0.2506 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= 0.136 Angle : 0.541 4.967 2637 Z= 0.283 Chirality : 0.041 0.115 312 Planarity : 0.003 0.033 308 Dihedral : 4.449 21.830 247 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.97 % Allowed : 15.76 % Favored : 82.27 % 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: 1.19 (0.55), residues: 226 helix: 1.40 (0.36), residues: 188 sheet: None (None), residues: 0 loop : -2.26 (1.04), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 944 HIS 0.003 0.001 HIS A1036 PHE 0.012 0.001 PHE A1185 TYR 0.006 0.001 TYR A 953 ARG 0.001 0.000 ARG A 896 Details of bonding type rmsd hydrogen bonds : bond 0.03532 ( 141) hydrogen bonds : angle 3.90993 ( 423) SS BOND : bond 0.00236 ( 2) SS BOND : angle 1.04395 ( 4) covalent geometry : bond 0.00322 ( 1943) covalent geometry : angle 0.53991 ( 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 22 residues out of total 203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 18 time to evaluate : 0.197 Fit side-chains REVERT: A 1021 LEU cc_start: 0.3683 (OUTLIER) cc_final: 0.3102 (tt) outliers start: 4 outliers final: 2 residues processed: 21 average time/residue: 0.0955 time to fit residues: 2.6777 Evaluate side-chains 19 residues out of total 203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 16 time to evaluate : 0.196 ------------------------------------------------------------------------------- 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 1202 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 20 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 10 optimal weight: 0.4980 chunk 3 optimal weight: 0.0270 chunk 13 optimal weight: 0.1980 chunk 4 optimal weight: 0.5980 chunk 21 optimal weight: 0.0970 chunk 8 optimal weight: 0.5980 overall best weight: 0.2836 ------------------------------------------------------------------------------- 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 = 0.4547 r_free = 0.4547 target = 0.247443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.206810 restraints weight = 2158.471| |-----------------------------------------------------------------------------| r_work (start): 0.4227 rms_B_bonded: 2.25 r_work: 0.4102 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.4102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5690 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 1945 Z= 0.114 Angle : 0.504 5.655 2637 Z= 0.264 Chirality : 0.039 0.103 312 Planarity : 0.003 0.032 308 Dihedral : 4.201 20.557 247 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.46 % Allowed : 15.76 % Favored : 81.77 % 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: 1.60 (0.56), residues: 226 helix: 1.72 (0.37), residues: 187 sheet: None (None), residues: 0 loop : -2.20 (0.99), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 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 0.03269 ( 141) hydrogen bonds : angle 3.72864 ( 423) SS BOND : bond 0.00189 ( 2) SS BOND : angle 0.87775 ( 4) covalent geometry : bond 0.00261 ( 1943) covalent geometry : angle 0.50336 ( 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 23 residues out of total 203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 18 time to evaluate : 0.198 Fit side-chains revert: symmetry clash REVERT: A 1021 LEU cc_start: 0.3540 (OUTLIER) cc_final: 0.2950 (tt) outliers start: 5 outliers final: 4 residues processed: 23 average time/residue: 0.0990 time to fit residues: 3.0101 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 : 0.214 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 10 optimal weight: 0.2980 chunk 12 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 16 optimal weight: 0.0870 chunk 3 optimal weight: 0.2980 chunk 5 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 22 optimal weight: 0.4980 overall best weight: 0.3758 ------------------------------------------------------------------------------- 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 = 0.4535 r_free = 0.4535 target = 0.245910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.205046 restraints weight = 2104.008| |-----------------------------------------------------------------------------| r_work (start): 0.4213 rms_B_bonded: 2.24 r_work: 0.4088 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.4088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5721 moved from start: 0.2791 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= 0.126 Angle : 0.525 5.837 2637 Z= 0.273 Chirality : 0.040 0.104 312 Planarity : 0.003 0.031 308 Dihedral : 4.234 21.178 247 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.97 % Allowed : 17.24 % Favored : 80.79 % 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: 1.72 (0.56), residues: 226 helix: 1.81 (0.37), residues: 187 sheet: None (None), residues: 0 loop : -2.21 (0.99), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 944 HIS 0.003 0.001 HIS A1036 PHE 0.012 0.001 PHE A1185 TYR 0.007 0.001 TYR A 953 ARG 0.002 0.000 ARG A 896 Details of bonding type rmsd hydrogen bonds : bond 0.03429 ( 141) hydrogen bonds : angle 3.71197 ( 423) SS BOND : bond 0.00200 ( 2) SS BOND : angle 0.94479 ( 4) covalent geometry : bond 0.00296 ( 1943) covalent geometry : angle 0.52396 ( 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 22 residues out of total 203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 18 time to evaluate : 0.205 Fit side-chains REVERT: A 1021 LEU cc_start: 0.3389 (OUTLIER) cc_final: 0.2802 (tt) outliers start: 4 outliers final: 3 residues processed: 22 average time/residue: 0.0916 time to fit residues: 2.7131 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 : 0.203 ------------------------------------------------------------------------------- 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 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: 0.0870 chunk 17 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 2 optimal weight: 0.0670 chunk 19 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 overall best weight: 0.3896 ------------------------------------------------------------------------------- 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 = 0.4533 r_free = 0.4533 target = 0.246403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.210803 restraints weight = 2171.140| |-----------------------------------------------------------------------------| r_work (start): 0.4269 rms_B_bonded: 2.17 r_work: 0.4096 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.4096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5739 moved from start: 0.2912 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= 0.130 Angle : 0.548 5.834 2637 Z= 0.282 Chirality : 0.040 0.120 312 Planarity : 0.003 0.031 308 Dihedral : 4.237 21.086 247 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.96 % Allowed : 17.73 % Favored : 79.31 % 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: 1.79 (0.55), residues: 226 helix: 1.90 (0.37), residues: 186 sheet: None (None), residues: 0 loop : -2.33 (0.89), 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 0.012 0.001 PHE A1185 TYR 0.007 0.001 TYR A 953 ARG 0.002 0.000 ARG A 896 Details of bonding type rmsd hydrogen bonds : bond 0.03462 ( 141) hydrogen bonds : angle 3.69198 ( 423) SS BOND : bond 0.00207 ( 2) SS BOND : angle 0.94625 ( 4) covalent geometry : bond 0.00310 ( 1943) covalent geometry : angle 0.54749 ( 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 24 residues out of total 203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 18 time to evaluate : 0.202 Fit side-chains revert: symmetry clash REVERT: A 1021 LEU cc_start: 0.3490 (OUTLIER) cc_final: 0.2930 (tt) outliers start: 6 outliers final: 4 residues processed: 24 average time/residue: 0.0907 time to fit residues: 2.9138 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 : 0.206 ------------------------------------------------------------------------------- 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: 0.4980 chunk 4 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 16 optimal weight: 0.0570 chunk 7 optimal weight: 0.5980 chunk 22 optimal weight: 0.2980 chunk 5 optimal weight: 0.3980 overall best weight: 0.3698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1192 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 = 0.4542 r_free = 0.4542 target = 0.246795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.210635 restraints weight = 2160.543| |-----------------------------------------------------------------------------| r_work (start): 0.4274 rms_B_bonded: 2.25 r_work: 0.4101 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.4101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5733 moved from start: 0.2967 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= 0.131 Angle : 0.555 5.947 2637 Z= 0.284 Chirality : 0.041 0.167 312 Planarity : 0.003 0.031 308 Dihedral : 4.237 20.868 247 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.46 % Allowed : 18.23 % Favored : 79.31 % 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: 1.74 (0.54), residues: 226 helix: 1.87 (0.36), residues: 186 sheet: None (None), residues: 0 loop : -2.41 (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 0.012 0.001 PHE A1185 TYR 0.008 0.001 TYR A 953 ARG 0.002 0.000 ARG A 896 Details of bonding type rmsd hydrogen bonds : bond 0.03539 ( 141) hydrogen bonds : angle 3.72185 ( 423) SS BOND : bond 0.00193 ( 2) SS BOND : angle 0.94234 ( 4) covalent geometry : bond 0.00311 ( 1943) covalent geometry : angle 0.55458 ( 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 24 residues out of total 203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 19 time to evaluate : 0.200 Fit side-chains revert: symmetry clash REVERT: A 1001 LEU cc_start: 0.6836 (tp) cc_final: 0.6343 (tp) outliers start: 5 outliers final: 4 residues processed: 24 average time/residue: 0.0951 time to fit residues: 3.0249 Evaluate side-chains 22 residues out of total 203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 18 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 918 ILE 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: 1.9990 chunk 13 optimal weight: 0.1980 chunk 22 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 5 optimal weight: 0.4980 chunk 0 optimal weight: 7.9990 chunk 2 optimal weight: 0.2980 chunk 6 optimal weight: 0.8980 chunk 21 optimal weight: 0.4980 chunk 14 optimal weight: 0.7980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1192 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 = 0.4531 r_free = 0.4531 target = 0.245684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.210461 restraints weight = 2129.571| |-----------------------------------------------------------------------------| r_work (start): 0.4267 rms_B_bonded: 2.12 r_work: 0.4094 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.4094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5738 moved from start: 0.3087 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= 0.139 Angle : 0.584 5.909 2637 Z= 0.294 Chirality : 0.042 0.162 312 Planarity : 0.003 0.031 308 Dihedral : 4.328 21.469 247 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.97 % Allowed : 18.23 % 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: 1.70 (0.54), residues: 226 helix: 1.85 (0.36), residues: 186 sheet: None (None), residues: 0 loop : -2.47 (0.87), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 944 HIS 0.003 0.001 HIS A1036 PHE 0.012 0.002 PHE A1185 TYR 0.012 0.001 TYR A 953 ARG 0.002 0.000 ARG A 896 Details of bonding type rmsd hydrogen bonds : bond 0.03597 ( 141) hydrogen bonds : angle 3.75214 ( 423) SS BOND : bond 0.00195 ( 2) SS BOND : angle 0.99094 ( 4) covalent geometry : bond 0.00333 ( 1943) covalent geometry : angle 0.58303 ( 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 22 residues out of total 203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 18 time to evaluate : 0.200 Fit side-chains revert: symmetry clash REVERT: A 1001 LEU cc_start: 0.6888 (tp) cc_final: 0.6439 (tp) outliers start: 4 outliers final: 3 residues processed: 22 average time/residue: 0.0909 time to fit residues: 2.6778 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 : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 5 optimal weight: 1.9990 chunk 16 optimal weight: 0.0670 chunk 21 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 12 optimal weight: 0.2980 chunk 6 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1192 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 = 0.4531 r_free = 0.4531 target = 0.245604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.210655 restraints weight = 2131.704| |-----------------------------------------------------------------------------| r_work (start): 0.4266 rms_B_bonded: 2.08 r_work: 0.4094 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.4094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5750 moved from start: 0.3134 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= 0.144 Angle : 0.591 6.021 2637 Z= 0.298 Chirality : 0.042 0.159 312 Planarity : 0.003 0.030 308 Dihedral : 4.356 21.585 247 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.48 % Allowed : 18.23 % 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: 1.68 (0.54), residues: 226 helix: 1.83 (0.36), residues: 186 sheet: None (None), residues: 0 loop : -2.45 (0.87), 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 0.012 0.002 PHE A1185 TYR 0.010 0.001 TYR A 953 ARG 0.003 0.000 ARG A 896 Details of bonding type rmsd hydrogen bonds : bond 0.03637 ( 141) hydrogen bonds : angle 3.78378 ( 423) SS BOND : bond 0.00208 ( 2) SS BOND : angle 1.02701 ( 4) covalent geometry : bond 0.00345 ( 1943) covalent geometry : angle 0.59038 ( 2633) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1587.87 seconds wall clock time: 28 minutes 21.75 seconds (1701.75 seconds total)