Starting phenix.real_space_refine on Wed Sep 17 03:37:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9u3s_63826/09_2025/9u3s_63826.cif Found real_map, /net/cci-nas-00/data/ceres_data/9u3s_63826/09_2025/9u3s_63826.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9u3s_63826/09_2025/9u3s_63826.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9u3s_63826/09_2025/9u3s_63826.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9u3s_63826/09_2025/9u3s_63826.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9u3s_63826/09_2025/9u3s_63826.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.005 sd= 0.048 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 23 5.16 5 C 2249 2.51 5 N 541 2.21 5 O 571 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3384 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3384 Classifications: {'peptide': 425} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 15, 'TRANS': 409} Chain breaks: 6 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 18 Time building chain proxies: 0.97, per 1000 atoms: 0.29 Number of scatterers: 3384 At special positions: 0 Unit cell: (51.51, 76.76, 84.84, 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 23 16.00 O 571 8.00 N 541 7.00 C 2249 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 217 " - pdb=" SG CYS A 268 " 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: 0.27 Conformation dependent library (CDL) restraints added in 127.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 816 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 0 sheets defined 88.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'A' and resid 98 through 138 Proline residue: A 110 - end of helix Processing helix chain 'A' and resid 146 through 165 removed outlier: 3.545A pdb=" N LEU A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N PHE A 164 " --> pdb=" O PHE A 160 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR A 165 " --> pdb=" O LEU A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 171 removed outlier: 3.765A pdb=" N ALA A 169 " --> pdb=" O THR A 165 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG A 170 " --> pdb=" O LYS A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 194 removed outlier: 3.627A pdb=" N GLN A 193 " --> pdb=" O ALA A 189 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N VAL A 194 " --> pdb=" O ALA A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 237 removed outlier: 3.757A pdb=" N SER A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 263 Processing helix chain 'A' and resid 279 through 321 removed outlier: 3.544A pdb=" N LYS A 321 " --> pdb=" O ILE A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 765 removed outlier: 3.542A pdb=" N THR A 765 " --> pdb=" O ARG A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 765 through 774 Processing helix chain 'A' and resid 782 through 809 removed outlier: 3.519A pdb=" N CYS A 805 " --> pdb=" O LEU A 801 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR A 809 " --> pdb=" O CYS A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 844 Processing helix chain 'A' and resid 849 through 860 removed outlier: 3.793A pdb=" N LEU A 855 " --> pdb=" O CYS A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 882 removed outlier: 3.829A pdb=" N ILE A 871 " --> pdb=" O CYS A 867 " (cutoff:3.500A) Proline residue: A 876 - end of helix Processing helix chain 'A' and resid 883 through 884 No H-bonds generated for 'chain 'A' and resid 883 through 884' Processing helix chain 'A' and resid 885 through 889 removed outlier: 4.557A pdb=" N GLU A 889 " --> pdb=" O SER A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 908 removed outlier: 3.798A pdb=" N ILE A 904 " --> pdb=" O SER A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 911 No H-bonds generated for 'chain 'A' and resid 909 through 911' Processing helix chain 'A' and resid 916 through 928 Processing helix chain 'A' and resid 929 through 937 removed outlier: 3.792A pdb=" N VAL A 937 " --> pdb=" O LEU A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 1020 277 hydrogen bonds defined for protein. 828 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: 0.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1014 1.34 - 1.46: 937 1.46 - 1.58: 1494 1.58 - 1.70: 0 1.70 - 1.81: 31 Bond restraints: 3476 Sorted by residual: bond pdb=" C VAL A 237 " pdb=" O VAL A 237 " ideal model delta sigma weight residual 1.241 1.226 0.015 1.25e-02 6.40e+03 1.43e+00 bond pdb=" CG1 ILE A 291 " pdb=" CD1 ILE A 291 " ideal model delta sigma weight residual 1.513 1.471 0.042 3.90e-02 6.57e+02 1.15e+00 bond pdb=" CB VAL A 907 " pdb=" CG1 VAL A 907 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.51e-01 bond pdb=" CB ASN A 774 " pdb=" CG ASN A 774 " ideal model delta sigma weight residual 1.516 1.539 -0.023 2.50e-02 1.60e+03 8.43e-01 bond pdb=" CB TRP A 858 " pdb=" CG TRP A 858 " ideal model delta sigma weight residual 1.498 1.526 -0.028 3.10e-02 1.04e+03 8.32e-01 ... (remaining 3471 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 4665 2.11 - 4.22: 45 4.22 - 6.33: 14 6.33 - 8.44: 1 8.44 - 10.55: 2 Bond angle restraints: 4727 Sorted by residual: angle pdb=" CB MET A 301 " pdb=" CG MET A 301 " pdb=" SD MET A 301 " ideal model delta sigma weight residual 112.70 121.77 -9.07 3.00e+00 1.11e-01 9.13e+00 angle pdb=" CA LEU A1016 " pdb=" CB LEU A1016 " pdb=" CG LEU A1016 " ideal model delta sigma weight residual 116.30 126.85 -10.55 3.50e+00 8.16e-02 9.09e+00 angle pdb=" CA GLU A 102 " pdb=" CB GLU A 102 " pdb=" CG GLU A 102 " ideal model delta sigma weight residual 114.10 120.03 -5.93 2.00e+00 2.50e-01 8.79e+00 angle pdb=" CG LYS A1020 " pdb=" CD LYS A1020 " pdb=" CE LYS A1020 " ideal model delta sigma weight residual 111.30 117.25 -5.95 2.30e+00 1.89e-01 6.69e+00 angle pdb=" N VAL A 144 " pdb=" CA VAL A 144 " pdb=" CB VAL A 144 " ideal model delta sigma weight residual 112.35 108.93 3.42 1.38e+00 5.25e-01 6.16e+00 ... (remaining 4722 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.33: 1651 16.33 - 32.65: 243 32.65 - 48.97: 82 48.97 - 65.30: 20 65.30 - 81.62: 7 Dihedral angle restraints: 2003 sinusoidal: 751 harmonic: 1252 Sorted by residual: dihedral pdb=" CB ARG A 284 " pdb=" CG ARG A 284 " pdb=" CD ARG A 284 " pdb=" NE ARG A 284 " ideal model delta sinusoidal sigma weight residual -180.00 -123.30 -56.70 3 1.50e+01 4.44e-03 9.41e+00 dihedral pdb=" N ARG A 139 " pdb=" CA ARG A 139 " pdb=" CB ARG A 139 " pdb=" CG ARG A 139 " ideal model delta sinusoidal sigma weight residual -60.00 -113.50 53.50 3 1.50e+01 4.44e-03 9.21e+00 dihedral pdb=" N ARG A 998 " pdb=" CA ARG A 998 " pdb=" CB ARG A 998 " pdb=" CG ARG A 998 " ideal model delta sinusoidal sigma weight residual -60.00 -113.44 53.44 3 1.50e+01 4.44e-03 9.20e+00 ... (remaining 2000 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 353 0.029 - 0.057: 148 0.057 - 0.086: 40 0.086 - 0.115: 12 0.115 - 0.144: 4 Chirality restraints: 557 Sorted by residual: chirality pdb=" CB VAL A 237 " pdb=" CA VAL A 237 " pdb=" CG1 VAL A 237 " pdb=" CG2 VAL A 237 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 5.15e-01 chirality pdb=" CA ILE A 747 " pdb=" N ILE A 747 " pdb=" C ILE A 747 " pdb=" CB ILE A 747 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.84e-01 chirality pdb=" CA PRO A 864 " pdb=" N PRO A 864 " pdb=" C PRO A 864 " pdb=" CB PRO A 864 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.69e-01 ... (remaining 554 not shown) Planarity restraints: 570 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 930 " 0.037 5.00e-02 4.00e+02 5.62e-02 5.05e+00 pdb=" N PRO A 931 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 931 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 931 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 774 " -0.011 2.00e-02 2.50e+03 2.23e-02 4.98e+00 pdb=" C ASN A 774 " 0.039 2.00e-02 2.50e+03 pdb=" O ASN A 774 " -0.015 2.00e-02 2.50e+03 pdb=" N SER A 775 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 782 " -0.025 5.00e-02 4.00e+02 3.77e-02 2.28e+00 pdb=" N PRO A 783 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 783 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 783 " -0.021 5.00e-02 4.00e+02 ... (remaining 567 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 69 2.70 - 3.25: 3657 3.25 - 3.80: 5636 3.80 - 4.35: 7273 4.35 - 4.90: 11762 Nonbonded interactions: 28397 Sorted by model distance: nonbonded pdb=" O SER A 762 " pdb=" OG SER A 766 " model vdw 2.147 3.040 nonbonded pdb=" OE1 GLU A 770 " pdb=" OG1 THR A 784 " model vdw 2.211 3.040 nonbonded pdb=" O ASN A 774 " pdb=" ND2 ASN A 774 " model vdw 2.218 3.120 nonbonded pdb=" NH2 ARG A 141 " pdb=" O THR A 216 " model vdw 2.302 3.120 nonbonded pdb=" OH TYR A 809 " pdb=" O HIS A 883 " model vdw 2.303 3.040 ... (remaining 28392 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: 0.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 4.710 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 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 0.042 3477 Z= 0.139 Angle : 0.622 10.554 4729 Z= 0.310 Chirality : 0.036 0.144 557 Planarity : 0.005 0.056 570 Dihedral : 18.337 81.624 1184 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 1.09 % Allowed : 34.78 % Favored : 64.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.43), residues: 411 helix: 0.74 (0.27), residues: 340 sheet: None (None), residues: 0 loop : 0.60 (0.98), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1005 TYR 0.025 0.002 TYR A 763 PHE 0.011 0.001 PHE A 121 TRP 0.005 0.001 TRP A 858 HIS 0.003 0.001 HIS A1009 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 3476) covalent geometry : angle 0.62180 ( 4727) SS BOND : bond 0.00004 ( 1) SS BOND : angle 0.24107 ( 2) hydrogen bonds : bond 0.22987 ( 277) hydrogen bonds : angle 8.07350 ( 828) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 101 time to evaluate : 0.117 Fit side-chains REVERT: A 998 ARG cc_start: 0.7754 (OUTLIER) cc_final: 0.7420 (tmm-80) REVERT: A 1002 VAL cc_start: 0.8889 (m) cc_final: 0.8643 (p) outliers start: 4 outliers final: 3 residues processed: 102 average time/residue: 0.0840 time to fit residues: 9.8718 Evaluate side-chains 102 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 98 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 MET Chi-restraints excluded: chain A residue 760 GLU Chi-restraints excluded: chain A residue 774 ASN Chi-restraints excluded: chain A residue 998 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 9.9990 chunk 30 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.147961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.132253 restraints weight = 4225.277| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 1.75 r_work: 0.3616 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3462 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 3477 Z= 0.147 Angle : 0.585 7.853 4729 Z= 0.296 Chirality : 0.038 0.132 557 Planarity : 0.005 0.054 570 Dihedral : 5.655 58.457 466 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 3.26 % Allowed : 29.89 % Favored : 66.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.88 (0.42), residues: 411 helix: 1.53 (0.26), residues: 350 sheet: None (None), residues: 0 loop : -0.13 (1.03), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1018 TYR 0.020 0.002 TYR A 763 PHE 0.009 0.001 PHE A 310 TRP 0.012 0.001 TRP A 994 HIS 0.004 0.001 HIS A 866 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 3476) covalent geometry : angle 0.58473 ( 4727) SS BOND : bond 0.00036 ( 1) SS BOND : angle 0.16734 ( 2) hydrogen bonds : bond 0.03837 ( 277) hydrogen bonds : angle 4.79619 ( 828) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 0.121 Fit side-chains REVERT: A 146 VAL cc_start: 0.7714 (OUTLIER) cc_final: 0.7429 (t) REVERT: A 229 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7641 (mt-10) REVERT: A 252 TYR cc_start: 0.7921 (t80) cc_final: 0.7498 (t80) REVERT: A 262 HIS cc_start: 0.6238 (OUTLIER) cc_final: 0.5882 (m90) REVERT: A 823 VAL cc_start: 0.8859 (t) cc_final: 0.8529 (t) REVERT: A 840 ARG cc_start: 0.8279 (mtp85) cc_final: 0.7616 (ttp80) REVERT: A 874 SER cc_start: 0.7625 (t) cc_final: 0.7336 (m) REVERT: A 998 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7712 (ttm-80) REVERT: A 1002 VAL cc_start: 0.9000 (m) cc_final: 0.8800 (p) REVERT: A 1004 TYR cc_start: 0.8490 (t80) cc_final: 0.8241 (t80) outliers start: 12 outliers final: 2 residues processed: 117 average time/residue: 0.0755 time to fit residues: 10.4134 Evaluate side-chains 108 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 103 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 262 HIS Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 998 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 2 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 19 optimal weight: 0.0170 chunk 5 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 overall best weight: 1.1624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.147647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.131524 restraints weight = 4223.467| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 1.80 r_work: 0.3594 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3440 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3477 Z= 0.155 Angle : 0.551 8.186 4729 Z= 0.279 Chirality : 0.037 0.130 557 Planarity : 0.005 0.054 570 Dihedral : 4.733 50.431 458 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 5.16 % Allowed : 28.26 % Favored : 66.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.25 (0.42), residues: 411 helix: 1.82 (0.26), residues: 350 sheet: None (None), residues: 0 loop : -0.26 (1.02), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1018 TYR 0.012 0.001 TYR A 763 PHE 0.011 0.001 PHE A 780 TRP 0.010 0.001 TRP A 858 HIS 0.004 0.001 HIS A 866 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 3476) covalent geometry : angle 0.55107 ( 4727) SS BOND : bond 0.00017 ( 1) SS BOND : angle 0.12944 ( 2) hydrogen bonds : bond 0.03623 ( 277) hydrogen bonds : angle 4.53047 ( 828) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 0.092 Fit side-chains REVERT: A 252 TYR cc_start: 0.8006 (t80) cc_final: 0.7626 (t80) REVERT: A 313 VAL cc_start: 0.8256 (t) cc_final: 0.8019 (t) REVERT: A 840 ARG cc_start: 0.8158 (mtp85) cc_final: 0.7522 (mtp85) REVERT: A 874 SER cc_start: 0.7757 (t) cc_final: 0.7534 (m) REVERT: A 909 TYR cc_start: 0.8340 (m-80) cc_final: 0.7828 (m-80) REVERT: A 998 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7721 (ttm-80) REVERT: A 1002 VAL cc_start: 0.8966 (m) cc_final: 0.8750 (p) REVERT: A 1004 TYR cc_start: 0.8424 (t80) cc_final: 0.7856 (t80) outliers start: 19 outliers final: 9 residues processed: 116 average time/residue: 0.0813 time to fit residues: 11.0593 Evaluate side-chains 117 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 780 PHE Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 980 GLN Chi-restraints excluded: chain A residue 998 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 39 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 29 optimal weight: 0.0370 chunk 12 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 10 optimal weight: 0.0470 chunk 16 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 overall best weight: 0.5760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.149194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.133213 restraints weight = 4182.177| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 1.79 r_work: 0.3621 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3472 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3477 Z= 0.122 Angle : 0.531 9.117 4729 Z= 0.263 Chirality : 0.036 0.137 557 Planarity : 0.005 0.052 570 Dihedral : 4.503 42.891 458 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 4.62 % Allowed : 28.53 % Favored : 66.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.48 (0.42), residues: 411 helix: 1.99 (0.27), residues: 351 sheet: None (None), residues: 0 loop : -0.31 (1.04), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1005 TYR 0.013 0.001 TYR A 763 PHE 0.014 0.001 PHE A 263 TRP 0.010 0.001 TRP A 994 HIS 0.003 0.001 HIS A 288 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 3476) covalent geometry : angle 0.53155 ( 4727) SS BOND : bond 0.00020 ( 1) SS BOND : angle 0.07737 ( 2) hydrogen bonds : bond 0.03188 ( 277) hydrogen bonds : angle 4.32810 ( 828) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.122 Fit side-chains REVERT: A 146 VAL cc_start: 0.7661 (OUTLIER) cc_final: 0.7407 (t) REVERT: A 226 MET cc_start: 0.7947 (mtt) cc_final: 0.7618 (mtm) REVERT: A 232 PHE cc_start: 0.8421 (OUTLIER) cc_final: 0.8091 (m-80) REVERT: A 252 TYR cc_start: 0.7930 (t80) cc_final: 0.7575 (t80) REVERT: A 313 VAL cc_start: 0.8275 (t) cc_final: 0.8058 (t) REVERT: A 840 ARG cc_start: 0.8164 (mtp85) cc_final: 0.7696 (mtp85) REVERT: A 874 SER cc_start: 0.7752 (t) cc_final: 0.7527 (m) REVERT: A 904 ILE cc_start: 0.8774 (mt) cc_final: 0.8568 (mt) REVERT: A 921 SER cc_start: 0.8573 (m) cc_final: 0.8116 (p) REVERT: A 1002 VAL cc_start: 0.8924 (m) cc_final: 0.8702 (p) REVERT: A 1004 TYR cc_start: 0.8351 (t80) cc_final: 0.7748 (t80) outliers start: 17 outliers final: 8 residues processed: 122 average time/residue: 0.0807 time to fit residues: 11.5633 Evaluate side-chains 114 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 104 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 284 ARG Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 780 PHE Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 980 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 13 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.148006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.132554 restraints weight = 4199.989| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 1.73 r_work: 0.3613 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3464 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3477 Z= 0.141 Angle : 0.548 9.029 4729 Z= 0.274 Chirality : 0.037 0.124 557 Planarity : 0.005 0.052 570 Dihedral : 3.588 13.758 454 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 4.89 % Allowed : 29.89 % Favored : 65.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.61 (0.42), residues: 411 helix: 2.07 (0.27), residues: 350 sheet: None (None), residues: 0 loop : -0.25 (1.02), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1005 TYR 0.012 0.001 TYR A 763 PHE 0.011 0.001 PHE A 780 TRP 0.008 0.001 TRP A 994 HIS 0.003 0.001 HIS A 288 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 3476) covalent geometry : angle 0.54833 ( 4727) SS BOND : bond 0.00015 ( 1) SS BOND : angle 0.16333 ( 2) hydrogen bonds : bond 0.03246 ( 277) hydrogen bonds : angle 4.28784 ( 828) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.096 Fit side-chains REVERT: A 146 VAL cc_start: 0.7695 (OUTLIER) cc_final: 0.7461 (t) REVERT: A 226 MET cc_start: 0.7973 (mtt) cc_final: 0.7630 (mtm) REVERT: A 232 PHE cc_start: 0.8402 (OUTLIER) cc_final: 0.8107 (m-80) REVERT: A 252 TYR cc_start: 0.7976 (t80) cc_final: 0.7569 (t80) REVERT: A 313 VAL cc_start: 0.8246 (t) cc_final: 0.8032 (t) REVERT: A 763 TYR cc_start: 0.8260 (t80) cc_final: 0.7984 (t80) REVERT: A 840 ARG cc_start: 0.8131 (mtp85) cc_final: 0.7864 (mtp85) REVERT: A 874 SER cc_start: 0.7848 (t) cc_final: 0.7603 (m) REVERT: A 904 ILE cc_start: 0.8799 (mt) cc_final: 0.8585 (mt) REVERT: A 921 SER cc_start: 0.8567 (m) cc_final: 0.8135 (p) REVERT: A 1002 VAL cc_start: 0.8951 (m) cc_final: 0.8739 (p) REVERT: A 1004 TYR cc_start: 0.8354 (t80) cc_final: 0.7849 (t80) outliers start: 18 outliers final: 9 residues processed: 116 average time/residue: 0.0829 time to fit residues: 11.2884 Evaluate side-chains 112 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 780 PHE Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 980 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 2 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 38 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 9 optimal weight: 7.9990 chunk 12 optimal weight: 0.0770 chunk 14 optimal weight: 0.9990 overall best weight: 1.3544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.147266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.131565 restraints weight = 4151.309| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 1.75 r_work: 0.3594 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3442 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 3477 Z= 0.166 Angle : 0.578 9.652 4729 Z= 0.285 Chirality : 0.038 0.137 557 Planarity : 0.005 0.052 570 Dihedral : 3.648 13.899 454 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 5.43 % Allowed : 28.80 % Favored : 65.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.49 (0.42), residues: 411 helix: 2.00 (0.27), residues: 351 sheet: None (None), residues: 0 loop : -0.41 (1.00), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1005 TYR 0.016 0.002 TYR A 763 PHE 0.014 0.001 PHE A 780 TRP 0.008 0.001 TRP A 858 HIS 0.004 0.001 HIS A 288 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 3476) covalent geometry : angle 0.57789 ( 4727) SS BOND : bond 0.00021 ( 1) SS BOND : angle 0.18942 ( 2) hydrogen bonds : bond 0.03369 ( 277) hydrogen bonds : angle 4.35418 ( 828) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 0.129 Fit side-chains REVERT: A 146 VAL cc_start: 0.7671 (OUTLIER) cc_final: 0.7438 (t) REVERT: A 232 PHE cc_start: 0.8425 (OUTLIER) cc_final: 0.8124 (m-80) REVERT: A 313 VAL cc_start: 0.8233 (t) cc_final: 0.8016 (t) REVERT: A 840 ARG cc_start: 0.8142 (mtp85) cc_final: 0.7855 (mtp85) REVERT: A 874 SER cc_start: 0.7955 (t) cc_final: 0.7671 (m) REVERT: A 904 ILE cc_start: 0.8835 (mt) cc_final: 0.8616 (mt) REVERT: A 921 SER cc_start: 0.8572 (m) cc_final: 0.8192 (p) REVERT: A 1002 VAL cc_start: 0.8920 (m) cc_final: 0.8686 (p) REVERT: A 1004 TYR cc_start: 0.8410 (t80) cc_final: 0.8033 (t80) outliers start: 20 outliers final: 14 residues processed: 113 average time/residue: 0.0836 time to fit residues: 11.0307 Evaluate side-chains 116 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 227 CYS Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 780 PHE Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 980 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 18 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 12 optimal weight: 0.0770 chunk 28 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.148573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.133201 restraints weight = 4214.996| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 1.72 r_work: 0.3623 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3475 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3477 Z= 0.127 Angle : 0.560 10.111 4729 Z= 0.273 Chirality : 0.036 0.147 557 Planarity : 0.005 0.051 570 Dihedral : 3.580 14.433 454 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 5.43 % Allowed : 29.35 % Favored : 65.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.60 (0.42), residues: 411 helix: 2.10 (0.27), residues: 350 sheet: None (None), residues: 0 loop : -0.45 (0.98), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1005 TYR 0.018 0.002 TYR A 763 PHE 0.011 0.001 PHE A 192 TRP 0.009 0.001 TRP A 994 HIS 0.003 0.001 HIS A 288 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 3476) covalent geometry : angle 0.56038 ( 4727) SS BOND : bond 0.00026 ( 1) SS BOND : angle 0.04729 ( 2) hydrogen bonds : bond 0.03115 ( 277) hydrogen bonds : angle 4.25857 ( 828) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.129 Fit side-chains REVERT: A 107 ARG cc_start: 0.7626 (OUTLIER) cc_final: 0.7422 (mmm160) REVERT: A 115 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.8490 (mtt180) REVERT: A 146 VAL cc_start: 0.7671 (OUTLIER) cc_final: 0.7429 (t) REVERT: A 226 MET cc_start: 0.7960 (mtt) cc_final: 0.7611 (mtm) REVERT: A 232 PHE cc_start: 0.8358 (OUTLIER) cc_final: 0.8093 (m-80) REVERT: A 313 VAL cc_start: 0.8161 (t) cc_final: 0.7954 (t) REVERT: A 840 ARG cc_start: 0.8078 (mtp85) cc_final: 0.7808 (mtp85) REVERT: A 874 SER cc_start: 0.7903 (t) cc_final: 0.7651 (m) REVERT: A 904 ILE cc_start: 0.8818 (mt) cc_final: 0.8592 (mt) REVERT: A 921 SER cc_start: 0.8533 (m) cc_final: 0.8122 (p) REVERT: A 1002 VAL cc_start: 0.8928 (m) cc_final: 0.8698 (p) REVERT: A 1004 TYR cc_start: 0.8364 (t80) cc_final: 0.7830 (t80) outliers start: 20 outliers final: 13 residues processed: 115 average time/residue: 0.0902 time to fit residues: 12.0311 Evaluate side-chains 118 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 227 CYS Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 780 PHE Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 980 GLN Chi-restraints excluded: chain A residue 996 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 8.9990 chunk 21 optimal weight: 0.7980 chunk 41 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 883 HIS ** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.146832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.131306 restraints weight = 4213.884| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 1.73 r_work: 0.3599 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3444 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 3477 Z= 0.162 Angle : 0.583 9.958 4729 Z= 0.285 Chirality : 0.038 0.152 557 Planarity : 0.005 0.062 570 Dihedral : 3.656 14.592 454 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 5.43 % Allowed : 29.89 % Favored : 64.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.51 (0.42), residues: 411 helix: 2.01 (0.27), residues: 351 sheet: None (None), residues: 0 loop : -0.36 (1.03), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A1005 TYR 0.012 0.002 TYR A 122 PHE 0.014 0.001 PHE A 780 TRP 0.009 0.001 TRP A 858 HIS 0.004 0.001 HIS A 288 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 3476) covalent geometry : angle 0.58273 ( 4727) SS BOND : bond 0.00020 ( 1) SS BOND : angle 0.19569 ( 2) hydrogen bonds : bond 0.03293 ( 277) hydrogen bonds : angle 4.32165 ( 828) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.123 Fit side-chains REVERT: A 107 ARG cc_start: 0.7586 (OUTLIER) cc_final: 0.7371 (mmm160) REVERT: A 115 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.8525 (mtt180) REVERT: A 146 VAL cc_start: 0.7691 (OUTLIER) cc_final: 0.7458 (t) REVERT: A 229 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7742 (mt-10) REVERT: A 232 PHE cc_start: 0.8363 (OUTLIER) cc_final: 0.8097 (m-80) REVERT: A 840 ARG cc_start: 0.8122 (mtp85) cc_final: 0.7834 (mtp85) REVERT: A 874 SER cc_start: 0.7974 (t) cc_final: 0.7704 (m) REVERT: A 904 ILE cc_start: 0.8847 (mt) cc_final: 0.8635 (mt) REVERT: A 921 SER cc_start: 0.8561 (m) cc_final: 0.8213 (p) REVERT: A 1002 VAL cc_start: 0.8926 (m) cc_final: 0.8687 (p) REVERT: A 1004 TYR cc_start: 0.8354 (t80) cc_final: 0.7930 (t80) outliers start: 20 outliers final: 15 residues processed: 112 average time/residue: 0.0824 time to fit residues: 10.8060 Evaluate side-chains 118 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 227 CYS Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 780 PHE Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 980 GLN Chi-restraints excluded: chain A residue 996 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 7 optimal weight: 0.9980 chunk 38 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 32 optimal weight: 0.4980 chunk 17 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.148233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.132638 restraints weight = 4205.158| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 1.76 r_work: 0.3615 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3462 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3477 Z= 0.134 Angle : 0.582 9.993 4729 Z= 0.281 Chirality : 0.037 0.153 557 Planarity : 0.004 0.051 570 Dihedral : 3.591 14.944 454 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 5.16 % Allowed : 30.71 % Favored : 64.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.55 (0.42), residues: 411 helix: 2.06 (0.27), residues: 350 sheet: None (None), residues: 0 loop : -0.47 (1.01), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 305 TYR 0.010 0.001 TYR A 122 PHE 0.011 0.001 PHE A 780 TRP 0.008 0.001 TRP A 994 HIS 0.003 0.001 HIS A 288 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 3476) covalent geometry : angle 0.58195 ( 4727) SS BOND : bond 0.00009 ( 1) SS BOND : angle 0.07696 ( 2) hydrogen bonds : bond 0.03134 ( 277) hydrogen bonds : angle 4.26096 ( 828) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 0.165 Fit side-chains REVERT: A 115 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.8517 (mtt180) REVERT: A 146 VAL cc_start: 0.7664 (OUTLIER) cc_final: 0.7423 (t) REVERT: A 232 PHE cc_start: 0.8348 (OUTLIER) cc_final: 0.8080 (m-80) REVERT: A 840 ARG cc_start: 0.8084 (mtp85) cc_final: 0.7804 (mtp85) REVERT: A 874 SER cc_start: 0.7941 (t) cc_final: 0.7655 (m) REVERT: A 904 ILE cc_start: 0.8803 (mt) cc_final: 0.8575 (mt) REVERT: A 920 ARG cc_start: 0.8548 (mtm110) cc_final: 0.8342 (mtm180) REVERT: A 921 SER cc_start: 0.8536 (m) cc_final: 0.8140 (p) REVERT: A 1002 VAL cc_start: 0.8932 (m) cc_final: 0.8703 (p) REVERT: A 1004 TYR cc_start: 0.8321 (t80) cc_final: 0.7907 (t80) outliers start: 19 outliers final: 13 residues processed: 116 average time/residue: 0.0836 time to fit residues: 11.3102 Evaluate side-chains 118 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 227 CYS Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 780 PHE Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 996 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 0.0970 chunk 7 optimal weight: 0.9990 chunk 14 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 chunk 33 optimal weight: 0.4980 chunk 35 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 26 optimal weight: 0.0970 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.149361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.134040 restraints weight = 4245.604| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 1.72 r_work: 0.3634 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3482 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3477 Z= 0.118 Angle : 0.569 9.926 4729 Z= 0.273 Chirality : 0.036 0.155 557 Planarity : 0.004 0.050 570 Dihedral : 3.524 15.212 454 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 4.89 % Allowed : 30.71 % Favored : 64.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.63 (0.42), residues: 411 helix: 2.12 (0.27), residues: 350 sheet: None (None), residues: 0 loop : -0.48 (1.01), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1018 TYR 0.011 0.001 TYR A 122 PHE 0.010 0.001 PHE A 192 TRP 0.011 0.001 TRP A 994 HIS 0.003 0.001 HIS A 288 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 3476) covalent geometry : angle 0.56869 ( 4727) SS BOND : bond 0.00006 ( 1) SS BOND : angle 0.04264 ( 2) hydrogen bonds : bond 0.02997 ( 277) hydrogen bonds : angle 4.23202 ( 828) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.129 Fit side-chains revert: symmetry clash REVERT: A 115 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.8499 (mtt180) REVERT: A 146 VAL cc_start: 0.7650 (OUTLIER) cc_final: 0.7418 (t) REVERT: A 226 MET cc_start: 0.7928 (mtt) cc_final: 0.7587 (mtm) REVERT: A 229 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7636 (mt-10) REVERT: A 232 PHE cc_start: 0.8350 (OUTLIER) cc_final: 0.8103 (m-80) REVERT: A 242 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.6887 (pt) REVERT: A 313 VAL cc_start: 0.8135 (t) cc_final: 0.7932 (t) REVERT: A 840 ARG cc_start: 0.8057 (mtp85) cc_final: 0.7785 (mtp85) REVERT: A 874 SER cc_start: 0.7915 (t) cc_final: 0.7641 (m) REVERT: A 904 ILE cc_start: 0.8737 (mt) cc_final: 0.8517 (mt) REVERT: A 920 ARG cc_start: 0.8483 (mtm110) cc_final: 0.8233 (ttp-110) REVERT: A 921 SER cc_start: 0.8499 (m) cc_final: 0.8096 (p) REVERT: A 998 ARG cc_start: 0.8145 (tmm-80) cc_final: 0.7777 (mtp85) REVERT: A 1002 VAL cc_start: 0.8938 (m) cc_final: 0.8716 (p) REVERT: A 1004 TYR cc_start: 0.8207 (t80) cc_final: 0.7830 (t80) outliers start: 18 outliers final: 12 residues processed: 117 average time/residue: 0.0849 time to fit residues: 11.5649 Evaluate side-chains 118 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 227 CYS Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 996 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 25 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 5 optimal weight: 0.3980 chunk 29 optimal weight: 0.0670 chunk 23 optimal weight: 0.3980 chunk 40 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 GLN ** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.149872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.134773 restraints weight = 4292.099| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 1.72 r_work: 0.3646 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3495 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3477 Z= 0.118 Angle : 0.573 9.858 4729 Z= 0.274 Chirality : 0.036 0.157 557 Planarity : 0.004 0.050 570 Dihedral : 3.546 15.561 454 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 4.62 % Allowed : 30.71 % Favored : 64.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.65 (0.43), residues: 411 helix: 2.17 (0.27), residues: 348 sheet: None (None), residues: 0 loop : -0.58 (0.98), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1005 TYR 0.010 0.001 TYR A 122 PHE 0.010 0.001 PHE A 192 TRP 0.011 0.001 TRP A 994 HIS 0.003 0.001 HIS A 288 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 3476) covalent geometry : angle 0.57323 ( 4727) SS BOND : bond 0.00014 ( 1) SS BOND : angle 0.08460 ( 2) hydrogen bonds : bond 0.02925 ( 277) hydrogen bonds : angle 4.22962 ( 828) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 951.44 seconds wall clock time: 16 minutes 58.42 seconds (1018.42 seconds total)