Starting phenix.real_space_refine on Wed Mar 5 14:39:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jmt_36426/03_2025/8jmt_36426_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jmt_36426/03_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_36426/03_2025/8jmt_36426.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jmt_36426/03_2025/8jmt_36426.map" model { file = "/net/cci-nas-00/data/ceres_data/8jmt_36426/03_2025/8jmt_36426_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jmt_36426/03_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-5624/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: 2.09, per 1000 atoms: 1.10 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: 0.41 Conformation dependent library (CDL) restraints added in 221.1 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: 0.18 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: 0.50 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: 0.740 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: 0.010 Set scattering table: 0.020 Process input model: 10.120 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.810 ------------------------------------------------------------------------------- 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 1943 Z= 0.196 Angle : 0.745 8.952 2633 Z= 0.456 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 *********************** 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 : 0.187 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: 0.0846 time to fit residues: 2.1254 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 : 0.189 ------------------------------------------------------------------------------- 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 1943 Z= 0.207 Angle : 0.588 6.020 2633 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 *********************** 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 : 0.177 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0934 time to fit residues: 2.1889 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 : 0.204 ------------------------------------------------------------------------------- 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 1943 Z= 0.245 Angle : 0.593 5.973 2633 Z= 0.312 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 *********************** 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 : 0.184 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: 0.1068 time to fit residues: 2.4486 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 : 0.192 ------------------------------------------------------------------------------- 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 1943 Z= 0.251 Angle : 0.587 6.277 2633 Z= 0.309 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 *********************** 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 : 0.188 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: 0.1004 time to fit residues: 2.5694 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 : 0.203 ------------------------------------------------------------------------------- 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: 0.0070 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: 0.7980 chunk 1 optimal weight: 1.9990 chunk 22 optimal weight: 0.4980 chunk 6 optimal weight: 0.7980 chunk 16 optimal weight: 0.3980 chunk 18 optimal weight: 1.9990 overall best weight: 0.4198 ------------------------------------------------------------------------------- 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 = 0.4639 r_free = 0.4639 target = 0.254156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.214685 restraints weight = 2176.685| |-----------------------------------------------------------------------------| r_work (start): 0.4212 rms_B_bonded: 2.28 r_work: 0.4087 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.4087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5744 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 1943 Z= 0.200 Angle : 0.536 4.964 2633 Z= 0.281 Chirality : 0.040 0.114 312 Planarity : 0.003 0.033 308 Dihedral : 4.428 21.699 247 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 8.82 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: 1.21 (0.56), residues: 226 helix: 1.42 (0.36), residues: 188 sheet: None (None), residues: 0 loop : -2.25 (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 967 *********************** 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 23 residues out of total 203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 19 time to evaluate : 0.200 Fit side-chains REVERT: A 977 MET cc_start: 0.3876 (tpp) cc_final: 0.3667 (ttm) REVERT: A 1021 LEU cc_start: 0.3723 (OUTLIER) cc_final: 0.3133 (tt) outliers start: 4 outliers final: 2 residues processed: 22 average time/residue: 0.0935 time to fit residues: 2.7455 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 : 0.202 ------------------------------------------------------------------------------- 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: 0.7980 chunk 15 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 10 optimal weight: 0.0050 chunk 3 optimal weight: 0.0370 chunk 13 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 21 optimal weight: 0.0970 chunk 8 optimal weight: 0.8980 overall best weight: 0.3270 ------------------------------------------------------------------------------- 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 = 0.4651 r_free = 0.4651 target = 0.256280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.217840 restraints weight = 2197.143| |-----------------------------------------------------------------------------| r_work (start): 0.4233 rms_B_bonded: 2.16 r_work: 0.4110 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.4110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5712 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 1943 Z= 0.175 Angle : 0.514 5.547 2633 Z= 0.270 Chirality : 0.039 0.102 312 Planarity : 0.003 0.032 308 Dihedral : 4.224 20.773 247 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 : 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: 1.59 (0.56), residues: 226 helix: 1.71 (0.37), residues: 187 sheet: None (None), residues: 0 loop : -2.24 (0.97), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 944 HIS 0.002 0.001 HIS A1036 PHE 0.012 0.001 PHE A1185 TYR 0.006 0.001 TYR A 953 ARG 0.001 0.000 ARG A 967 *********************** 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 24 residues out of total 203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 19 time to evaluate : 0.245 Fit side-chains revert: symmetry clash REVERT: A 1021 LEU cc_start: 0.3608 (OUTLIER) cc_final: 0.3006 (tt) outliers start: 5 outliers final: 4 residues processed: 24 average time/residue: 0.1147 time to fit residues: 3.6136 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 : 0.226 ------------------------------------------------------------------------------- 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: 0.8980 chunk 12 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 17 optimal weight: 0.3980 chunk 16 optimal weight: 0.5980 chunk 3 optimal weight: 0.0670 chunk 5 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 overall best weight: 0.4718 ------------------------------------------------------------------------------- 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 = 0.4512 r_free = 0.4512 target = 0.243104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.202638 restraints weight = 2098.710| |-----------------------------------------------------------------------------| r_work (start): 0.4195 rms_B_bonded: 2.21 r_work: 0.4072 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.4072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5740 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 1943 Z= 0.217 Angle : 0.563 5.778 2633 Z= 0.290 Chirality : 0.041 0.115 312 Planarity : 0.003 0.032 308 Dihedral : 4.410 22.534 247 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 10.12 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: 1.54 (0.55), residues: 226 helix: 1.69 (0.37), residues: 186 sheet: None (None), residues: 0 loop : -2.21 (0.96), 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 0.013 0.002 PHE A 888 TYR 0.008 0.001 TYR A 953 ARG 0.002 0.000 ARG A 896 *********************** 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 21 residues out of total 203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 17 time to evaluate : 0.206 Fit side-chains REVERT: A 1021 LEU cc_start: 0.3446 (OUTLIER) cc_final: 0.2884 (tt) outliers start: 4 outliers final: 3 residues processed: 21 average time/residue: 0.0896 time to fit residues: 2.5627 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 : 0.180 ------------------------------------------------------------------------------- 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: 0.0970 chunk 17 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 9 optimal weight: 0.3980 chunk 21 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 2 optimal weight: 0.0770 chunk 19 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 overall best weight: 0.3736 ------------------------------------------------------------------------------- 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 = 0.4537 r_free = 0.4537 target = 0.246474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.211134 restraints weight = 2167.165| |-----------------------------------------------------------------------------| r_work (start): 0.4273 rms_B_bonded: 2.15 r_work: 0.4102 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.4102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5802 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 1943 Z= 0.191 Angle : 0.543 5.792 2633 Z= 0.280 Chirality : 0.040 0.122 312 Planarity : 0.003 0.031 308 Dihedral : 4.249 20.931 247 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.96 % Allowed : 17.24 % 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: 1.74 (0.55), residues: 226 helix: 1.87 (0.37), residues: 186 sheet: None (None), residues: 0 loop : -2.40 (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 0.006 0.001 TYR A 953 ARG 0.002 0.000 ARG A 896 *********************** 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 : 0.199 Fit side-chains revert: symmetry clash REVERT: A 1001 LEU cc_start: 0.6872 (tp) cc_final: 0.6369 (tp) REVERT: A 1021 LEU cc_start: 0.3622 (OUTLIER) cc_final: 0.3043 (tt) outliers start: 6 outliers final: 4 residues processed: 24 average time/residue: 0.0938 time to fit residues: 2.9807 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 : 0.202 ------------------------------------------------------------------------------- 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: 0.5980 chunk 4 optimal weight: 0.9980 chunk 11 optimal weight: 0.0870 chunk 19 optimal weight: 0.0770 chunk 3 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 16 optimal weight: 0.3980 chunk 7 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 overall best weight: 0.3516 ------------------------------------------------------------------------------- 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 = 0.4539 r_free = 0.4539 target = 0.246633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.211551 restraints weight = 2175.003| |-----------------------------------------------------------------------------| r_work (start): 0.4278 rms_B_bonded: 2.10 r_work: 0.4111 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.4111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5769 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 1943 Z= 0.187 Angle : 0.546 5.975 2633 Z= 0.279 Chirality : 0.041 0.170 312 Planarity : 0.003 0.031 308 Dihedral : 4.242 20.993 247 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 8.04 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: 1.73 (0.55), residues: 226 helix: 1.88 (0.36), residues: 186 sheet: None (None), residues: 0 loop : -2.48 (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 0.006 0.001 TYR A 971 ARG 0.002 0.000 ARG A 896 *********************** 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 : 0.217 Fit side-chains revert: symmetry clash REVERT: A 1001 LEU cc_start: 0.6944 (tp) cc_final: 0.6458 (tp) REVERT: A 1021 LEU cc_start: 0.3664 (OUTLIER) cc_final: 0.3067 (tt) outliers start: 5 outliers final: 3 residues processed: 22 average time/residue: 0.0975 time to fit residues: 2.8788 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 : 0.212 ------------------------------------------------------------------------------- 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 10 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 2 optimal weight: 0.4980 chunk 6 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 14 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: A1192 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.242156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.208278 restraints weight = 2131.561| |-----------------------------------------------------------------------------| r_work (start): 0.4249 rms_B_bonded: 2.09 r_work: 0.4088 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.4088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5875 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 1943 Z= 0.262 Angle : 0.635 6.818 2633 Z= 0.323 Chirality : 0.044 0.159 312 Planarity : 0.003 0.031 308 Dihedral : 4.619 23.379 247 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 9.08 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: 1.29 (0.54), residues: 226 helix: 1.55 (0.36), residues: 187 sheet: None (None), residues: 0 loop : -2.59 (0.91), residues: 39 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 A 888 TYR 0.009 0.001 TYR A 953 ARG 0.003 0.001 ARG A 896 ********************** 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: 4 poor density : 19 time to evaluate : 0.201 Fit side-chains revert: symmetry clash REVERT: A 1001 LEU cc_start: 0.7018 (tp) cc_final: 0.6513 (tp) REVERT: A 1021 LEU cc_start: 0.3621 (OUTLIER) cc_final: 0.3013 (tt) outliers start: 4 outliers final: 3 residues processed: 23 average time/residue: 0.0915 time to fit residues: 2.8135 Evaluate side-chains 23 residues out of total 203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 19 time to evaluate : 0.197 ------------------------------------------------------------------------------- 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: 0.7980 chunk 9 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 5 optimal weight: 0.4980 chunk 16 optimal weight: 0.1980 chunk 21 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 6 optimal weight: 8.9990 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... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.243022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.208944 restraints weight = 2117.664| |-----------------------------------------------------------------------------| r_work (start): 0.4261 rms_B_bonded: 1.96 r_work: 0.4100 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.4100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5843 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 1943 Z= 0.232 Angle : 0.604 5.922 2633 Z= 0.309 Chirality : 0.043 0.144 312 Planarity : 0.003 0.031 308 Dihedral : 4.493 22.086 247 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % 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: 1.42 (0.54), residues: 226 helix: 1.65 (0.36), residues: 186 sheet: None (None), residues: 0 loop : -2.50 (0.89), 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 A 888 TYR 0.008 0.001 TYR A 953 ARG 0.003 0.000 ARG A 896 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1450.02 seconds wall clock time: 25 minutes 50.92 seconds (1550.92 seconds total)