Starting phenix.real_space_refine on Wed Jul 23 12:10:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9u3s_63826/07_2025/9u3s_63826.cif Found real_map, /net/cci-nas-00/data/ceres_data/9u3s_63826/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9u3s_63826/07_2025/9u3s_63826.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9u3s_63826/07_2025/9u3s_63826.map" model { file = "/net/cci-nas-00/data/ceres_data/9u3s_63826/07_2025/9u3s_63826.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9u3s_63826/07_2025/9u3s_63826.cif" } resolution = 3.1 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= 0.005 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Time building chain proxies: 2.88, per 1000 atoms: 0.85 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: 1.07 Conformation dependent library (CDL) restraints added in 656.2 milliseconds 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: 0.37 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: 1.95 Time building geometry restraints manager: 1.10 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: 7.140 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 17.260 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:14.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.050 ------------------------------------------------------------------------------- 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 (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: 0.92 (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 TRP 0.005 0.001 TRP A 858 HIS 0.003 0.001 HIS A1009 PHE 0.011 0.001 PHE A 121 TYR 0.025 0.002 TYR A 763 ARG 0.011 0.001 ARG A1005 Details of bonding type rmsd hydrogen bonds : bond 0.22987 ( 277) hydrogen bonds : angle 8.07350 ( 828) SS BOND : bond 0.00004 ( 1) SS BOND : angle 0.24107 ( 2) covalent geometry : bond 0.00339 ( 3476) covalent geometry : angle 0.62180 ( 4727) *********************** 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 : 0.896 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: 0.4138 time to fit residues: 50.4490 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 : 0.508 ------------------------------------------------------------------------------- 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 35 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 12 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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 = 0.3921 r_free = 0.3921 target = 0.146865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.131351 restraints weight = 4159.159| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 1.72 r_work: 0.3601 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3451 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 3477 Z= 0.167 Angle : 0.595 8.238 4729 Z= 0.304 Chirality : 0.039 0.128 557 Planarity : 0.005 0.056 570 Dihedral : 5.709 59.326 466 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 3.26 % Allowed : 29.35 % Favored : 67.39 % 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: 1.84 (0.42), residues: 411 helix: 1.50 (0.26), residues: 350 sheet: None (None), residues: 0 loop : -0.15 (1.03), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 862 HIS 0.006 0.001 HIS A 866 PHE 0.010 0.001 PHE A 310 TYR 0.021 0.002 TYR A 763 ARG 0.009 0.001 ARG A 305 Details of bonding type rmsd hydrogen bonds : bond 0.03908 ( 277) hydrogen bonds : angle 4.83367 ( 828) SS BOND : bond 0.00016 ( 1) SS BOND : angle 0.17164 ( 2) covalent geometry : bond 0.00388 ( 3476) covalent geometry : angle 0.59516 ( 4727) *********************** 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 117 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 0.381 Fit side-chains REVERT: A 146 VAL cc_start: 0.7753 (OUTLIER) cc_final: 0.7480 (t) REVERT: A 229 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7664 (mt-10) REVERT: A 252 TYR cc_start: 0.7951 (t80) cc_final: 0.7558 (t80) REVERT: A 823 VAL cc_start: 0.8896 (t) cc_final: 0.8592 (t) REVERT: A 840 ARG cc_start: 0.8258 (mtp85) cc_final: 0.7572 (ttp80) REVERT: A 874 SER cc_start: 0.7687 (t) cc_final: 0.7440 (m) REVERT: A 909 TYR cc_start: 0.8284 (m-80) cc_final: 0.7820 (m-80) REVERT: A 998 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7686 (ttm-80) REVERT: A 1002 VAL cc_start: 0.8997 (m) cc_final: 0.8790 (p) REVERT: A 1004 TYR cc_start: 0.8483 (t80) cc_final: 0.8152 (t80) outliers start: 12 outliers final: 3 residues processed: 114 average time/residue: 0.3793 time to fit residues: 50.8823 Evaluate side-chains 107 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 102 time to evaluate : 0.418 ------------------------------------------------------------------------------- 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 885 THR Chi-restraints excluded: chain A residue 988 LEU 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 34 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 1 optimal weight: 0.3980 chunk 40 optimal weight: 0.7980 chunk 38 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3939 r_free = 0.3939 target = 0.148469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.132663 restraints weight = 4168.198| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 1.77 r_work: 0.3618 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3463 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3477 Z= 0.135 Angle : 0.543 8.615 4729 Z= 0.272 Chirality : 0.036 0.124 557 Planarity : 0.005 0.050 570 Dihedral : 4.742 50.728 458 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 5.71 % Allowed : 27.72 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.42), residues: 411 helix: 1.81 (0.26), residues: 351 sheet: None (None), residues: 0 loop : -0.28 (1.03), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 994 HIS 0.003 0.001 HIS A 866 PHE 0.007 0.001 PHE A 152 TYR 0.011 0.001 TYR A1004 ARG 0.006 0.001 ARG A1018 Details of bonding type rmsd hydrogen bonds : bond 0.03506 ( 277) hydrogen bonds : angle 4.49782 ( 828) SS BOND : bond 0.00043 ( 1) SS BOND : angle 0.08189 ( 2) covalent geometry : bond 0.00307 ( 3476) covalent geometry : angle 0.54322 ( 4727) *********************** 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 132 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 0.301 Fit side-chains REVERT: A 146 VAL cc_start: 0.7691 (OUTLIER) cc_final: 0.7438 (t) REVERT: A 232 PHE cc_start: 0.8399 (OUTLIER) cc_final: 0.8110 (m-80) REVERT: A 252 TYR cc_start: 0.7979 (t80) cc_final: 0.7632 (t80) REVERT: A 313 VAL cc_start: 0.8234 (t) cc_final: 0.8002 (t) REVERT: A 760 GLU cc_start: 0.7616 (tp30) cc_final: 0.7010 (tp30) REVERT: A 809 TYR cc_start: 0.7950 (m-10) cc_final: 0.7672 (m-80) REVERT: A 840 ARG cc_start: 0.8188 (mtp85) cc_final: 0.7549 (mtp85) REVERT: A 874 SER cc_start: 0.7703 (t) cc_final: 0.7479 (m) REVERT: A 998 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.7710 (ttm-80) REVERT: A 1002 VAL cc_start: 0.8976 (m) cc_final: 0.8767 (p) REVERT: A 1004 TYR cc_start: 0.8393 (t80) cc_final: 0.7750 (t80) outliers start: 21 outliers final: 10 residues processed: 123 average time/residue: 0.1925 time to fit residues: 27.8425 Evaluate side-chains 117 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 0.368 ------------------------------------------------------------------------------- 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 311 LEU Chi-restraints excluded: chain A residue 751 SER Chi-restraints excluded: chain A residue 780 PHE Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 980 GLN Chi-restraints excluded: chain A residue 988 LEU 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 37 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 14 optimal weight: 0.4980 chunk 25 optimal weight: 0.6980 chunk 15 optimal weight: 0.2980 chunk 32 optimal weight: 0.9980 chunk 30 optimal weight: 7.9990 chunk 24 optimal weight: 0.9990 chunk 33 optimal weight: 9.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3944 r_free = 0.3944 target = 0.148818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.132965 restraints weight = 4246.299| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 1.77 r_work: 0.3617 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3462 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3477 Z= 0.122 Angle : 0.532 9.243 4729 Z= 0.262 Chirality : 0.036 0.138 557 Planarity : 0.004 0.046 570 Dihedral : 4.498 42.884 458 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 4.08 % Allowed : 28.26 % Favored : 67.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.55 (0.42), residues: 411 helix: 2.02 (0.27), residues: 351 sheet: None (None), residues: 0 loop : -0.26 (1.04), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 994 HIS 0.003 0.001 HIS A 288 PHE 0.011 0.001 PHE A 263 TYR 0.011 0.001 TYR A 763 ARG 0.005 0.001 ARG A1005 Details of bonding type rmsd hydrogen bonds : bond 0.03216 ( 277) hydrogen bonds : angle 4.31424 ( 828) SS BOND : bond 0.00015 ( 1) SS BOND : angle 0.12742 ( 2) covalent geometry : bond 0.00284 ( 3476) covalent geometry : angle 0.53173 ( 4727) *********************** 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 118 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.337 Fit side-chains REVERT: A 146 VAL cc_start: 0.7672 (OUTLIER) cc_final: 0.7430 (t) REVERT: A 226 MET cc_start: 0.7920 (mtt) cc_final: 0.7605 (mtm) REVERT: A 232 PHE cc_start: 0.8436 (OUTLIER) cc_final: 0.8117 (m-80) REVERT: A 252 TYR cc_start: 0.7973 (t80) cc_final: 0.7533 (t80) REVERT: A 313 VAL cc_start: 0.8272 (t) cc_final: 0.8051 (t) REVERT: A 840 ARG cc_start: 0.8147 (mtp85) cc_final: 0.7683 (mtp85) REVERT: A 857 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7150 (mp0) REVERT: A 874 SER cc_start: 0.7733 (t) cc_final: 0.7517 (m) REVERT: A 921 SER cc_start: 0.8579 (m) cc_final: 0.8116 (p) REVERT: A 1002 VAL cc_start: 0.8895 (m) cc_final: 0.8675 (p) REVERT: A 1004 TYR cc_start: 0.8348 (t80) cc_final: 0.7737 (t80) outliers start: 15 outliers final: 6 residues processed: 114 average time/residue: 0.1895 time to fit residues: 25.1599 Evaluate side-chains 111 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 103 time to evaluate : 0.274 ------------------------------------------------------------------------------- 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 780 PHE Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 988 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 23 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 19 optimal weight: 0.0070 chunk 12 optimal weight: 0.7980 chunk 32 optimal weight: 0.0980 chunk 5 optimal weight: 0.6980 overall best weight: 0.4598 ------------------------------------------------------------------------------- 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 = 0.3960 r_free = 0.3960 target = 0.150115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.134314 restraints weight = 4219.176| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 1.76 r_work: 0.3632 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3477 Z= 0.117 Angle : 0.539 9.550 4729 Z= 0.265 Chirality : 0.035 0.123 557 Planarity : 0.005 0.060 570 Dihedral : 3.534 14.008 454 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 4.08 % Allowed : 30.16 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.74 (0.42), residues: 411 helix: 2.17 (0.27), residues: 351 sheet: None (None), residues: 0 loop : -0.29 (1.01), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 994 HIS 0.002 0.001 HIS A 288 PHE 0.010 0.001 PHE A 192 TYR 0.017 0.001 TYR A 763 ARG 0.010 0.001 ARG A1005 Details of bonding type rmsd hydrogen bonds : bond 0.03061 ( 277) hydrogen bonds : angle 4.17650 ( 828) SS BOND : bond 0.00032 ( 1) SS BOND : angle 0.03437 ( 2) covalent geometry : bond 0.00270 ( 3476) covalent geometry : angle 0.53869 ( 4727) *********************** 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: 15 poor density : 108 time to evaluate : 0.330 Fit side-chains REVERT: A 146 VAL cc_start: 0.7594 (OUTLIER) cc_final: 0.7377 (t) REVERT: A 226 MET cc_start: 0.7920 (mtt) cc_final: 0.7575 (mtm) REVERT: A 229 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7763 (mt-10) REVERT: A 232 PHE cc_start: 0.8384 (OUTLIER) cc_final: 0.8066 (m-80) REVERT: A 252 TYR cc_start: 0.7939 (t80) cc_final: 0.7440 (t80) REVERT: A 313 VAL cc_start: 0.8198 (t) cc_final: 0.7986 (t) REVERT: A 763 TYR cc_start: 0.8211 (t80) cc_final: 0.7910 (t80) REVERT: A 840 ARG cc_start: 0.8068 (mtp85) cc_final: 0.7567 (mtp85) REVERT: A 857 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7070 (mp0) REVERT: A 874 SER cc_start: 0.7747 (t) cc_final: 0.7533 (m) REVERT: A 909 TYR cc_start: 0.8349 (m-80) cc_final: 0.7812 (m-80) REVERT: A 921 SER cc_start: 0.8528 (m) cc_final: 0.8198 (m) REVERT: A 1002 VAL cc_start: 0.8951 (m) cc_final: 0.8724 (p) REVERT: A 1004 TYR cc_start: 0.8253 (t80) cc_final: 0.7735 (t80) outliers start: 15 outliers final: 5 residues processed: 117 average time/residue: 0.3071 time to fit residues: 42.7448 Evaluate side-chains 116 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 109 time to evaluate : 0.391 ------------------------------------------------------------------------------- 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 308 SER Chi-restraints excluded: chain A residue 780 PHE Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 988 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 7 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 = 0.3916 r_free = 0.3916 target = 0.146415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.130250 restraints weight = 4268.852| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 1.78 r_work: 0.3579 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3424 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 3477 Z= 0.183 Angle : 0.597 9.390 4729 Z= 0.295 Chirality : 0.039 0.142 557 Planarity : 0.005 0.058 570 Dihedral : 3.699 13.675 454 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 4.08 % Allowed : 31.52 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.54 (0.42), residues: 411 helix: 2.01 (0.26), residues: 351 sheet: None (None), residues: 0 loop : -0.23 (1.06), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 858 HIS 0.005 0.001 HIS A 288 PHE 0.013 0.001 PHE A 785 TYR 0.016 0.002 TYR A 763 ARG 0.013 0.001 ARG A1005 Details of bonding type rmsd hydrogen bonds : bond 0.03477 ( 277) hydrogen bonds : angle 4.34413 ( 828) SS BOND : bond 0.00031 ( 1) SS BOND : angle 0.30085 ( 2) covalent geometry : bond 0.00426 ( 3476) covalent geometry : angle 0.59739 ( 4727) *********************** 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 123 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 0.362 Fit side-chains REVERT: A 122 TYR cc_start: 0.8301 (t80) cc_final: 0.7791 (t80) REVERT: A 229 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7650 (mt-10) REVERT: A 313 VAL cc_start: 0.8246 (t) cc_final: 0.8044 (t) REVERT: A 840 ARG cc_start: 0.8149 (mtp85) cc_final: 0.7862 (mtp85) REVERT: A 874 SER cc_start: 0.7968 (t) cc_final: 0.7695 (m) REVERT: A 921 SER cc_start: 0.8572 (m) cc_final: 0.8211 (p) REVERT: A 1002 VAL cc_start: 0.8969 (m) cc_final: 0.8756 (p) REVERT: A 1004 TYR cc_start: 0.8436 (t80) cc_final: 0.7929 (t80) outliers start: 15 outliers final: 9 residues processed: 116 average time/residue: 0.1898 time to fit residues: 25.7560 Evaluate side-chains 119 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 110 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 CYS 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 885 THR Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 934 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 8 optimal weight: 0.7980 chunk 38 optimal weight: 6.9990 chunk 7 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3948 r_free = 0.3948 target = 0.148848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.133107 restraints weight = 4190.473| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 1.73 r_work: 0.3620 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3468 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.2723 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= 0.130 Angle : 0.575 10.083 4729 Z= 0.278 Chirality : 0.037 0.144 557 Planarity : 0.005 0.063 570 Dihedral : 3.634 13.899 454 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.49 (0.41), residues: 411 helix: 2.02 (0.27), residues: 355 sheet: None (None), residues: 0 loop : -0.76 (0.96), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 994 HIS 0.003 0.001 HIS A 866 PHE 0.010 0.001 PHE A 192 TYR 0.017 0.001 TYR A 763 ARG 0.013 0.001 ARG A1005 Details of bonding type rmsd hydrogen bonds : bond 0.03160 ( 277) hydrogen bonds : angle 4.25266 ( 828) SS BOND : bond 0.00011 ( 1) SS BOND : angle 0.06117 ( 2) covalent geometry : bond 0.00309 ( 3476) covalent geometry : angle 0.57518 ( 4727) *********************** 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 120 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.359 Fit side-chains REVERT: A 146 VAL cc_start: 0.7597 (OUTLIER) cc_final: 0.7377 (t) REVERT: A 226 MET cc_start: 0.7911 (mtt) cc_final: 0.7552 (mtm) REVERT: A 229 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7605 (mt-10) REVERT: A 232 PHE cc_start: 0.8393 (OUTLIER) cc_final: 0.8106 (m-80) REVERT: A 313 VAL cc_start: 0.8184 (t) cc_final: 0.7971 (t) REVERT: A 840 ARG cc_start: 0.8135 (mtp85) cc_final: 0.7842 (mtp85) REVERT: A 857 GLU cc_start: 0.7638 (mt-10) cc_final: 0.7288 (mp0) REVERT: A 874 SER cc_start: 0.7885 (t) cc_final: 0.7613 (m) REVERT: A 921 SER cc_start: 0.8537 (m) cc_final: 0.8148 (p) REVERT: A 1002 VAL cc_start: 0.8873 (m) cc_final: 0.8632 (p) REVERT: A 1004 TYR cc_start: 0.8360 (t80) cc_final: 0.7943 (t80) outliers start: 17 outliers final: 12 residues processed: 114 average time/residue: 0.1995 time to fit residues: 26.4612 Evaluate side-chains 116 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.336 ------------------------------------------------------------------------------- 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 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 853 LYS Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 988 LEU 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 8 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 23 optimal weight: 0.0470 chunk 14 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 33 optimal weight: 0.0980 overall best weight: 0.6078 ------------------------------------------------------------------------------- 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 = 0.3954 r_free = 0.3954 target = 0.149190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.133834 restraints weight = 4184.324| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 1.71 r_work: 0.3635 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3484 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3477 Z= 0.120 Angle : 0.565 10.228 4729 Z= 0.274 Chirality : 0.036 0.142 557 Planarity : 0.005 0.081 570 Dihedral : 3.594 14.505 454 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 9.45 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.60 (0.42), residues: 411 helix: 2.11 (0.27), residues: 355 sheet: None (None), residues: 0 loop : -0.77 (0.97), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 994 HIS 0.003 0.001 HIS A 288 PHE 0.009 0.001 PHE A 192 TYR 0.021 0.001 TYR A 763 ARG 0.015 0.001 ARG A1005 Details of bonding type rmsd hydrogen bonds : bond 0.03028 ( 277) hydrogen bonds : angle 4.18499 ( 828) SS BOND : bond 0.00020 ( 1) SS BOND : angle 0.05935 ( 2) covalent geometry : bond 0.00281 ( 3476) covalent geometry : angle 0.56532 ( 4727) *********************** 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 126 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 0.338 Fit side-chains REVERT: A 107 ARG cc_start: 0.7442 (OUTLIER) cc_final: 0.7220 (mmm160) REVERT: A 146 VAL cc_start: 0.7596 (OUTLIER) cc_final: 0.7378 (t) REVERT: A 226 MET cc_start: 0.7925 (mtt) cc_final: 0.7585 (mtm) REVERT: A 232 PHE cc_start: 0.8369 (OUTLIER) cc_final: 0.8104 (m-80) REVERT: A 313 VAL cc_start: 0.8129 (t) cc_final: 0.7928 (t) REVERT: A 840 ARG cc_start: 0.8115 (mtp85) cc_final: 0.7836 (mtp85) REVERT: A 857 GLU cc_start: 0.7629 (mt-10) cc_final: 0.7230 (mp0) REVERT: A 874 SER cc_start: 0.7878 (t) cc_final: 0.7616 (m) REVERT: A 921 SER cc_start: 0.8514 (m) cc_final: 0.8119 (p) REVERT: A 998 ARG cc_start: 0.8125 (tmm-80) cc_final: 0.7772 (mtp85) REVERT: A 1002 VAL cc_start: 0.8890 (m) cc_final: 0.8662 (p) REVERT: A 1004 TYR cc_start: 0.8294 (t80) cc_final: 0.7678 (t80) outliers start: 17 outliers final: 12 residues processed: 119 average time/residue: 0.1917 time to fit residues: 26.6019 Evaluate side-chains 119 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 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 853 LYS Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 988 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 37 optimal weight: 4.9990 chunk 9 optimal weight: 9.9990 chunk 41 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.3942 r_free = 0.3942 target = 0.148063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.132693 restraints weight = 4156.574| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 1.71 r_work: 0.3622 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3468 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.2896 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= 0.142 Angle : 0.609 9.967 4729 Z= 0.288 Chirality : 0.037 0.149 557 Planarity : 0.004 0.046 570 Dihedral : 3.588 14.955 454 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 4.08 % Allowed : 31.25 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.54 (0.42), residues: 411 helix: 2.06 (0.27), residues: 354 sheet: None (None), residues: 0 loop : -0.70 (0.96), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 994 HIS 0.004 0.001 HIS A 288 PHE 0.010 0.001 PHE A 192 TYR 0.015 0.001 TYR A 809 ARG 0.004 0.001 ARG A1005 Details of bonding type rmsd hydrogen bonds : bond 0.03115 ( 277) hydrogen bonds : angle 4.22336 ( 828) SS BOND : bond 0.00010 ( 1) SS BOND : angle 0.05367 ( 2) covalent geometry : bond 0.00338 ( 3476) covalent geometry : angle 0.60915 ( 4727) *********************** 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 121 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 106 time to evaluate : 0.364 Fit side-chains REVERT: A 115 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.8522 (mtt180) REVERT: A 232 PHE cc_start: 0.8391 (OUTLIER) cc_final: 0.8144 (m-80) REVERT: A 313 VAL cc_start: 0.8141 (t) cc_final: 0.7939 (t) REVERT: A 840 ARG cc_start: 0.8097 (mtp85) cc_final: 0.7800 (mtp85) REVERT: A 874 SER cc_start: 0.7940 (t) cc_final: 0.7672 (m) REVERT: A 921 SER cc_start: 0.8511 (m) cc_final: 0.8217 (p) REVERT: A 998 ARG cc_start: 0.8146 (tmm-80) cc_final: 0.7779 (mtp85) REVERT: A 1002 VAL cc_start: 0.8940 (m) cc_final: 0.8723 (p) REVERT: A 1004 TYR cc_start: 0.8296 (t80) cc_final: 0.7853 (t80) outliers start: 15 outliers final: 10 residues processed: 116 average time/residue: 0.1973 time to fit residues: 26.8160 Evaluate side-chains 118 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ARG 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 885 THR Chi-restraints excluded: chain A residue 934 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 27 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3943 r_free = 0.3943 target = 0.148200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.132453 restraints weight = 4223.935| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 1.76 r_work: 0.3610 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3456 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 3477 Z= 0.146 Angle : 0.608 10.001 4729 Z= 0.291 Chirality : 0.038 0.151 557 Planarity : 0.004 0.047 570 Dihedral : 3.610 15.250 454 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.53 % Allowed : 32.34 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.50 (0.42), residues: 411 helix: 2.04 (0.27), residues: 354 sheet: None (None), residues: 0 loop : -0.79 (0.95), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 994 HIS 0.004 0.001 HIS A 288 PHE 0.009 0.001 PHE A 780 TYR 0.016 0.002 TYR A 809 ARG 0.005 0.001 ARG A1005 Details of bonding type rmsd hydrogen bonds : bond 0.03149 ( 277) hydrogen bonds : angle 4.24879 ( 828) SS BOND : bond 0.00004 ( 1) SS BOND : angle 0.06393 ( 2) covalent geometry : bond 0.00346 ( 3476) covalent geometry : angle 0.60825 ( 4727) ********************** 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 116 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.334 Fit side-chains REVERT: A 115 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.8491 (mtt180) REVERT: A 232 PHE cc_start: 0.8385 (OUTLIER) cc_final: 0.8091 (m-80) REVERT: A 313 VAL cc_start: 0.8152 (t) cc_final: 0.7952 (t) REVERT: A 840 ARG cc_start: 0.8078 (mtp85) cc_final: 0.7789 (mtp85) REVERT: A 874 SER cc_start: 0.7944 (t) cc_final: 0.7668 (m) REVERT: A 921 SER cc_start: 0.8521 (m) cc_final: 0.8226 (p) REVERT: A 998 ARG cc_start: 0.8161 (tmm-80) cc_final: 0.7792 (mtp85) REVERT: A 1002 VAL cc_start: 0.8933 (m) cc_final: 0.8702 (p) REVERT: A 1004 TYR cc_start: 0.8277 (t80) cc_final: 0.7814 (t80) outliers start: 13 outliers final: 11 residues processed: 112 average time/residue: 0.1917 time to fit residues: 24.9803 Evaluate side-chains 116 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ARG 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 885 THR Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 934 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 26 optimal weight: 0.0040 chunk 5 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 29 optimal weight: 0.0070 chunk 24 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 overall best weight: 0.4812 ------------------------------------------------------------------------------- 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 = 0.3969 r_free = 0.3969 target = 0.150160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.134877 restraints weight = 4184.744| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 1.72 r_work: 0.3652 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3501 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3477 Z= 0.119 Angle : 0.599 10.027 4729 Z= 0.282 Chirality : 0.036 0.146 557 Planarity : 0.004 0.046 570 Dihedral : 3.519 15.402 454 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 3.80 % Allowed : 32.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.60 (0.42), residues: 411 helix: 2.11 (0.27), residues: 355 sheet: None (None), residues: 0 loop : -0.77 (0.96), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 994 HIS 0.002 0.001 HIS A 288 PHE 0.010 0.001 PHE A 192 TYR 0.015 0.001 TYR A 809 ARG 0.003 0.000 ARG A1005 Details of bonding type rmsd hydrogen bonds : bond 0.02938 ( 277) hydrogen bonds : angle 4.16451 ( 828) SS BOND : bond 0.00019 ( 1) SS BOND : angle 0.12104 ( 2) covalent geometry : bond 0.00280 ( 3476) covalent geometry : angle 0.59927 ( 4727) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2584.82 seconds wall clock time: 47 minutes 6.92 seconds (2826.92 seconds total)