Starting phenix.real_space_refine on Thu Mar 6 05:38:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xlt_33286/03_2025/7xlt_33286.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xlt_33286/03_2025/7xlt_33286.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xlt_33286/03_2025/7xlt_33286.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xlt_33286/03_2025/7xlt_33286.map" model { file = "/net/cci-nas-00/data/ceres_data/7xlt_33286/03_2025/7xlt_33286.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xlt_33286/03_2025/7xlt_33286.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.046 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: 5 Type Number sf(0) Gaussians P 78 5.49 5 S 14 5.16 5 C 2869 2.51 5 N 845 2.21 5 O 1179 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 4985 Number of models: 1 Model: "" Number of chains: 4 Chain: "H" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1635 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 11, 'TRANS': 203} Chain: "L" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1676 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 11, 'TRANS': 204} Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 801 Classifications: {'DNA': 40} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 39} Chain: "B" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 873 Classifications: {'RNA': 40} Modifications used: {'5*END': 1, 'rna3p_pur': 32, 'rna3p_pyr': 8} Link IDs: {'rna3p': 39} Time building chain proxies: 4.04, per 1000 atoms: 0.81 Number of scatterers: 4985 At special positions: 0 Unit cell: (125.465, 106.918, 93.826, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 78 15.00 O 1179 8.00 N 845 7.00 C 2869 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 146 " - pdb=" SG CYS H 201 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 93 " distance=2.04 Simple disulfide: pdb=" SG CYS L 139 " - pdb=" SG CYS L 199 " distance=2.04 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: 1.36 Conformation dependent library (CDL) restraints added in 486.0 milliseconds 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 796 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 9 sheets defined 5.6% alpha, 36.0% beta 41 base pairs and 55 stacking pairs defined. Time for finding SS restraints: 2.08 Creating SS restraints... Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.606A pdb=" N ASP H 90 " --> pdb=" O THR H 87 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 87 through 91' Processing helix chain 'H' and resid 176 through 180 Processing helix chain 'H' and resid 192 through 194 No H-bonds generated for 'chain 'H' and resid 192 through 194' Processing helix chain 'L' and resid 126 through 131 Processing helix chain 'L' and resid 188 through 192 Processing sheet with id=AA1, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.340A pdb=" N GLU H 10 " --> pdb=" O THR H 116 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N VAL H 33 " --> pdb=" O ASP H 99 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N MET H 34 " --> pdb=" O PHE H 50 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N PHE H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.340A pdb=" N GLU H 10 " --> pdb=" O THR H 116 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR H 108 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 126 through 129 removed outlier: 3.988A pdb=" N SER H 186 " --> pdb=" O HIS H 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 157 through 160 Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AA7, first strand: chain 'L' and resid 50 through 53 removed outlier: 5.817A pdb=" N LEU L 51 " --> pdb=" O LEU L 42 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N LEU L 42 " --> pdb=" O LEU L 51 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR L 107 " --> pdb=" O TYR L 91 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N CYS L 93 " --> pdb=" O GLY L 105 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N GLY L 105 " --> pdb=" O CYS L 93 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 119 through 123 Processing sheet with id=AA9, first strand: chain 'L' and resid 150 through 155 108 hydrogen bonds defined for protein. 264 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 102 hydrogen bonds 200 hydrogen bond angles 0 basepair planarities 41 basepair parallelities 55 stacking parallelities Total time for adding SS restraints: 1.70 Time building geometry restraints manager: 1.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1253 1.34 - 1.46: 1731 1.46 - 1.58: 2107 1.58 - 1.70: 156 1.70 - 1.82: 19 Bond restraints: 5266 Sorted by residual: bond pdb=" CA VAL L 99 " pdb=" CB VAL L 99 " ideal model delta sigma weight residual 1.534 1.551 -0.017 6.80e-03 2.16e+04 6.17e+00 bond pdb=" C GLU H 154 " pdb=" N PRO H 155 " ideal model delta sigma weight residual 1.334 1.386 -0.052 2.34e-02 1.83e+03 5.02e+00 bond pdb=" C VAL L 99 " pdb=" N PRO L 100 " ideal model delta sigma weight residual 1.334 1.386 -0.052 2.34e-02 1.83e+03 5.00e+00 bond pdb=" CA VAL L 99 " pdb=" C VAL L 99 " ideal model delta sigma weight residual 1.520 1.539 -0.019 8.80e-03 1.29e+04 4.68e+00 bond pdb=" O5' C B 10 " pdb=" C5' C B 10 " ideal model delta sigma weight residual 1.420 1.452 -0.032 1.50e-02 4.44e+03 4.65e+00 ... (remaining 5261 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 7219 2.07 - 4.14: 247 4.14 - 6.21: 41 6.21 - 8.29: 10 8.29 - 10.36: 3 Bond angle restraints: 7520 Sorted by residual: angle pdb=" C HIS L 98 " pdb=" N VAL L 99 " pdb=" CA VAL L 99 " ideal model delta sigma weight residual 120.24 123.82 -3.58 6.30e-01 2.52e+00 3.22e+01 angle pdb=" C PRO H 153 " pdb=" N GLU H 154 " pdb=" CA GLU H 154 " ideal model delta sigma weight residual 120.09 125.72 -5.63 1.25e+00 6.40e-01 2.03e+01 angle pdb=" CA VAL L 99 " pdb=" C VAL L 99 " pdb=" N PRO L 100 " ideal model delta sigma weight residual 121.00 123.99 -2.99 8.30e-01 1.45e+00 1.30e+01 angle pdb=" CA GLU H 82 " pdb=" CB GLU H 82 " pdb=" CG GLU H 82 " ideal model delta sigma weight residual 114.10 121.30 -7.20 2.00e+00 2.50e-01 1.30e+01 angle pdb=" CB MET L 180 " pdb=" CG MET L 180 " pdb=" SD MET L 180 " ideal model delta sigma weight residual 112.70 123.06 -10.36 3.00e+00 1.11e-01 1.19e+01 ... (remaining 7515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.74: 2374 15.74 - 31.49: 398 31.49 - 47.23: 133 47.23 - 62.97: 53 62.97 - 78.72: 33 Dihedral angle restraints: 2991 sinusoidal: 1743 harmonic: 1248 Sorted by residual: dihedral pdb=" CA ASN L 58 " pdb=" C ASN L 58 " pdb=" N ARG L 59 " pdb=" CA ARG L 59 " ideal model delta harmonic sigma weight residual 180.00 -155.04 -24.96 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA VAL H 156 " pdb=" C VAL H 156 " pdb=" N THR H 157 " pdb=" CA THR H 157 " ideal model delta harmonic sigma weight residual 180.00 -155.62 -24.38 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA TYR H 80 " pdb=" C TYR H 80 " pdb=" N MET H 81 " pdb=" CA MET H 81 " ideal model delta harmonic sigma weight residual 180.00 157.33 22.67 0 5.00e+00 4.00e-02 2.06e+01 ... (remaining 2988 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 807 0.086 - 0.172: 59 0.172 - 0.258: 4 0.258 - 0.344: 3 0.344 - 0.430: 1 Chirality restraints: 874 Sorted by residual: chirality pdb=" P C B 37 " pdb=" OP1 C B 37 " pdb=" OP2 C B 37 " pdb=" O5' C B 37 " both_signs ideal model delta sigma weight residual True 2.41 -2.84 -0.43 2.00e-01 2.50e+01 4.62e+00 chirality pdb=" CB ILE L 155 " pdb=" CA ILE L 155 " pdb=" CG1 ILE L 155 " pdb=" CG2 ILE L 155 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" P C B 10 " pdb=" OP1 C B 10 " pdb=" OP2 C B 10 " pdb=" O5' C B 10 " both_signs ideal model delta sigma weight residual True 2.41 -2.71 -0.30 2.00e-01 2.50e+01 2.30e+00 ... (remaining 871 not shown) Planarity restraints: 662 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR L 7 " -0.036 5.00e-02 4.00e+02 5.48e-02 4.81e+00 pdb=" N PRO L 8 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO L 8 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO L 8 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 108 " 0.016 2.00e-02 2.50e+03 1.50e-02 4.50e+00 pdb=" CG TYR H 108 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TYR H 108 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR H 108 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR H 108 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR H 108 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR H 108 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR H 108 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP H 107 " -0.009 2.00e-02 2.50e+03 1.92e-02 3.70e+00 pdb=" CG ASP H 107 " 0.033 2.00e-02 2.50e+03 pdb=" OD1 ASP H 107 " -0.012 2.00e-02 2.50e+03 pdb=" OD2 ASP H 107 " -0.012 2.00e-02 2.50e+03 ... (remaining 659 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1322 2.81 - 3.33: 3795 3.33 - 3.86: 9088 3.86 - 4.38: 9680 4.38 - 4.90: 15108 Nonbonded interactions: 38993 Sorted by model distance: nonbonded pdb=" O GLY H 8 " pdb=" OG1 THR H 113 " model vdw 2.288 3.040 nonbonded pdb=" OG SER H 141 " pdb=" O VAL H 189 " model vdw 2.326 3.040 nonbonded pdb=" OG SER L 57 " pdb=" O GLY L 69 " model vdw 2.337 3.040 nonbonded pdb=" OG SER L 25 " pdb=" O GLN L 27 " model vdw 2.353 3.040 nonbonded pdb=" NH1 ARG L 66 " pdb=" OE2 GLU L 84 " model vdw 2.369 3.120 ... (remaining 38988 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 group one per residue 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: 0.260 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.700 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5953 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 : 0.004 0.052 5266 Z= 0.259 Angle : 0.887 10.357 7520 Z= 0.482 Chirality : 0.050 0.430 874 Planarity : 0.006 0.055 662 Dihedral : 18.802 78.716 2183 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 0.79 % Allowed : 34.30 % Favored : 64.91 % 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: -2.19 (0.39), residues: 427 helix: -3.85 (0.81), residues: 12 sheet: 0.01 (0.39), residues: 188 loop : -2.75 (0.37), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP L 168 HIS 0.012 0.002 HIS H 35 PHE 0.024 0.002 PHE L 94 TYR 0.037 0.002 TYR H 108 ARG 0.009 0.001 ARG L 66 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 70 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 107 THR cc_start: 0.6878 (m) cc_final: 0.6517 (m) REVERT: L 144 PHE cc_start: 0.6641 (m-10) cc_final: 0.6319 (m-10) REVERT: L 171 GLN cc_start: 0.6884 (tp40) cc_final: 0.6116 (tp-100) outliers start: 3 outliers final: 1 residues processed: 71 average time/residue: 0.2876 time to fit residues: 25.7424 Evaluate side-chains 62 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 61 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 20.0000 chunk 37 optimal weight: 6.9990 chunk 21 optimal weight: 8.9990 chunk 12 optimal weight: 9.9990 chunk 25 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 29 optimal weight: 9.9990 chunk 45 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN H 202 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.138315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.111446 restraints weight = 32775.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.111104 restraints weight = 22835.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.111274 restraints weight = 18702.401| |-----------------------------------------------------------------------------| r_work (final): 0.3952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 5266 Z= 0.410 Angle : 0.821 9.076 7520 Z= 0.438 Chirality : 0.042 0.179 874 Planarity : 0.006 0.064 662 Dihedral : 16.760 74.066 1436 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 24.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % 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: -2.62 (0.38), residues: 427 helix: -3.79 (0.68), residues: 19 sheet: -0.50 (0.38), residues: 177 loop : -2.68 (0.37), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.004 TRP H 105 HIS 0.006 0.002 HIS H 35 PHE 0.030 0.003 PHE L 76 TYR 0.019 0.003 TYR L 91 ARG 0.007 0.001 ARG L 59 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: L 61 SER cc_start: 0.8674 (m) cc_final: 0.8188 (p) REVERT: L 78 LEU cc_start: 0.8916 (tt) cc_final: 0.8662 (tt) REVERT: L 92 TYR cc_start: 0.8091 (m-10) cc_final: 0.7705 (m-10) REVERT: L 129 GLN cc_start: 0.6573 (pt0) cc_final: 0.6087 (pm20) REVERT: L 144 PHE cc_start: 0.7653 (m-10) cc_final: 0.7421 (m-10) REVERT: L 149 ILE cc_start: 0.6896 (mm) cc_final: 0.6656 (mm) REVERT: L 180 MET cc_start: 0.7606 (mmm) cc_final: 0.7120 (mmm) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.3116 time to fit residues: 25.0116 Evaluate side-chains 47 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 1.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 47 optimal weight: 9.9990 chunk 36 optimal weight: 6.9990 chunk 49 optimal weight: 30.0000 chunk 13 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 46 optimal weight: 20.0000 chunk 35 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 39 optimal weight: 8.9990 chunk 9 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 129 GLN ** L 166 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 = 0.4476 r_free = 0.4476 target = 0.137052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.111880 restraints weight = 33977.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.110565 restraints weight = 26618.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.110899 restraints weight = 21128.479| |-----------------------------------------------------------------------------| r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 5266 Z= 0.281 Angle : 0.714 6.556 7520 Z= 0.383 Chirality : 0.039 0.168 874 Planarity : 0.006 0.050 662 Dihedral : 16.905 74.057 1436 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 24.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 0.26 % Allowed : 5.01 % Favored : 94.72 % 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: -2.58 (0.38), residues: 427 helix: -3.51 (0.76), residues: 19 sheet: -0.28 (0.40), residues: 169 loop : -2.78 (0.36), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 47 HIS 0.009 0.002 HIS H 35 PHE 0.018 0.002 PHE L 76 TYR 0.014 0.002 TYR H 54 ARG 0.006 0.001 ARG L 59 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 53 time to evaluate : 0.739 Fit side-chains revert: symmetry clash REVERT: H 45 LEU cc_start: 0.8555 (mm) cc_final: 0.8216 (mt) REVERT: L 42 LEU cc_start: 0.8516 (tp) cc_final: 0.8250 (tp) REVERT: L 50 LYS cc_start: 0.7550 (mmpt) cc_final: 0.7028 (mmmt) REVERT: L 61 SER cc_start: 0.8775 (m) cc_final: 0.8316 (p) REVERT: L 78 LEU cc_start: 0.9104 (tt) cc_final: 0.8896 (tt) REVERT: L 92 TYR cc_start: 0.8193 (m-10) cc_final: 0.7755 (m-10) REVERT: L 129 GLN cc_start: 0.6711 (pt0) cc_final: 0.6094 (pm20) REVERT: L 149 ILE cc_start: 0.6512 (mm) cc_final: 0.6257 (mm) outliers start: 1 outliers final: 1 residues processed: 54 average time/residue: 0.2039 time to fit residues: 14.8252 Evaluate side-chains 48 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 47 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 6 optimal weight: 5.9990 chunk 44 optimal weight: 10.0000 chunk 48 optimal weight: 9.9990 chunk 36 optimal weight: 8.9990 chunk 15 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 31 optimal weight: 0.9990 chunk 32 optimal weight: 10.0000 chunk 4 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.138508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.107501 restraints weight = 32699.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.109556 restraints weight = 20388.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.110600 restraints weight = 14846.179| |-----------------------------------------------------------------------------| r_work (final): 0.3981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5266 Z= 0.233 Angle : 0.663 6.564 7520 Z= 0.360 Chirality : 0.038 0.164 874 Planarity : 0.005 0.045 662 Dihedral : 16.824 73.902 1436 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 22.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % 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: -2.44 (0.39), residues: 427 helix: -3.64 (0.73), residues: 19 sheet: -0.18 (0.40), residues: 169 loop : -2.68 (0.37), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 109 HIS 0.002 0.001 HIS H 170 PHE 0.020 0.002 PHE L 76 TYR 0.019 0.002 TYR L 191 ARG 0.007 0.001 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.404 Fit side-chains REVERT: H 45 LEU cc_start: 0.8524 (mm) cc_final: 0.8241 (mt) REVERT: H 107 ASP cc_start: 0.6712 (p0) cc_final: 0.6480 (p0) REVERT: L 24 ARG cc_start: 0.7549 (tmt170) cc_final: 0.7314 (tmt170) REVERT: L 50 LYS cc_start: 0.7231 (mmpt) cc_final: 0.6703 (mmmt) REVERT: L 92 TYR cc_start: 0.8132 (m-80) cc_final: 0.7507 (m-10) REVERT: L 149 ILE cc_start: 0.6229 (mm) cc_final: 0.5998 (mm) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.2434 time to fit residues: 17.4494 Evaluate side-chains 46 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 48 optimal weight: 10.9990 chunk 25 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 chunk 29 optimal weight: 4.9990 chunk 36 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 11 optimal weight: 9.9990 chunk 16 optimal weight: 20.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.134696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.104301 restraints weight = 33072.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.106182 restraints weight = 21173.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.107111 restraints weight = 15595.841| |-----------------------------------------------------------------------------| r_work (final): 0.3933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.4209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 5266 Z= 0.280 Angle : 0.710 6.592 7520 Z= 0.380 Chirality : 0.039 0.164 874 Planarity : 0.005 0.048 662 Dihedral : 16.923 74.029 1436 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 25.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % 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: -2.51 (0.39), residues: 427 helix: -3.83 (0.70), residues: 19 sheet: -0.30 (0.40), residues: 173 loop : -2.67 (0.38), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP H 109 HIS 0.005 0.001 HIS H 35 PHE 0.018 0.002 PHE L 76 TYR 0.028 0.002 TYR H 27 ARG 0.003 0.001 ARG H 104 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.762 Fit side-chains REVERT: H 20 MET cc_start: 0.8140 (tpp) cc_final: 0.7770 (tpt) REVERT: H 107 ASP cc_start: 0.6948 (p0) cc_final: 0.6336 (p0) REVERT: L 42 LEU cc_start: 0.8562 (tp) cc_final: 0.8353 (tp) REVERT: L 149 ILE cc_start: 0.6449 (mm) cc_final: 0.6144 (mm) REVERT: L 180 MET cc_start: 0.7575 (mmm) cc_final: 0.6888 (tpp) REVERT: L 192 GLU cc_start: 0.7961 (mp0) cc_final: 0.7394 (tp30) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.2592 time to fit residues: 18.1082 Evaluate side-chains 44 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 26 optimal weight: 0.3980 chunk 48 optimal weight: 9.9990 chunk 43 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 chunk 3 optimal weight: 0.3980 chunk 41 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 15 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.137574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.111523 restraints weight = 33670.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.111245 restraints weight = 22669.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.111392 restraints weight = 18064.024| |-----------------------------------------------------------------------------| r_work (final): 0.3961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.4217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5266 Z= 0.206 Angle : 0.657 6.365 7520 Z= 0.354 Chirality : 0.039 0.250 874 Planarity : 0.005 0.045 662 Dihedral : 16.804 73.845 1436 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 20.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % 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: -2.36 (0.40), residues: 427 helix: -3.57 (0.79), residues: 19 sheet: -0.15 (0.40), residues: 169 loop : -2.58 (0.38), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP H 36 HIS 0.004 0.001 HIS H 35 PHE 0.017 0.002 PHE L 76 TYR 0.024 0.002 TYR L 191 ARG 0.005 0.001 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.424 Fit side-chains REVERT: H 107 ASP cc_start: 0.6811 (p0) cc_final: 0.6230 (p0) REVERT: L 42 LEU cc_start: 0.8613 (tp) cc_final: 0.8388 (tp) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.2011 time to fit residues: 13.7909 Evaluate side-chains 46 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 26 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 33 optimal weight: 0.9980 chunk 46 optimal weight: 30.0000 chunk 23 optimal weight: 5.9990 chunk 2 optimal weight: 0.6980 chunk 20 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 chunk 8 optimal weight: 7.9990 overall best weight: 4.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 166 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.132974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.102802 restraints weight = 32141.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.103140 restraints weight = 20699.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.104316 restraints weight = 15626.317| |-----------------------------------------------------------------------------| r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.4785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 5266 Z= 0.325 Angle : 0.743 8.811 7520 Z= 0.400 Chirality : 0.041 0.231 874 Planarity : 0.005 0.051 662 Dihedral : 16.968 74.124 1436 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 27.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.13 % Favored : 90.87 % Rotamer: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.40), residues: 427 helix: -3.29 (0.91), residues: 19 sheet: -0.51 (0.39), residues: 173 loop : -2.72 (0.39), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP H 36 HIS 0.008 0.002 HIS H 35 PHE 0.019 0.003 PHE L 76 TYR 0.017 0.002 TYR H 95 ARG 0.004 0.001 ARG L 59 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.435 Fit side-chains revert: symmetry clash REVERT: H 107 ASP cc_start: 0.6791 (p0) cc_final: 0.6482 (p0) REVERT: L 4 MET cc_start: 0.8517 (tmm) cc_final: 0.8288 (tmm) REVERT: L 94 PHE cc_start: 0.7335 (t80) cc_final: 0.7029 (t80) REVERT: L 180 MET cc_start: 0.7971 (tpp) cc_final: 0.7599 (tpp) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.1569 time to fit residues: 10.9972 Evaluate side-chains 43 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 28 optimal weight: 1.9990 chunk 49 optimal weight: 30.0000 chunk 16 optimal weight: 20.0000 chunk 36 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 1 optimal weight: 20.0000 chunk 41 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 46 optimal weight: 30.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 61 ASN ** H 205 HIS ** 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 = 0.4443 r_free = 0.4443 target = 0.134087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.107763 restraints weight = 33833.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.106596 restraints weight = 24090.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.106932 restraints weight = 20412.780| |-----------------------------------------------------------------------------| r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.4999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 5266 Z= 0.280 Angle : 0.713 6.629 7520 Z= 0.383 Chirality : 0.041 0.224 874 Planarity : 0.006 0.062 662 Dihedral : 17.037 74.040 1436 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 26.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % 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: -2.69 (0.39), residues: 427 helix: -3.20 (0.95), residues: 19 sheet: -0.46 (0.39), residues: 169 loop : -2.79 (0.38), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.004 TRP H 36 HIS 0.011 0.002 HIS H 35 PHE 0.026 0.003 PHE L 76 TYR 0.016 0.002 TYR H 100 ARG 0.008 0.001 ARG L 59 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.337 Fit side-chains REVERT: L 4 MET cc_start: 0.8505 (tmm) cc_final: 0.8229 (tmm) REVERT: L 42 LEU cc_start: 0.8743 (tp) cc_final: 0.8424 (tp) REVERT: L 180 MET cc_start: 0.7896 (tpp) cc_final: 0.7218 (mmm) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.2631 time to fit residues: 17.3912 Evaluate side-chains 43 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 7.9990 chunk 18 optimal weight: 8.9990 chunk 6 optimal weight: 3.9990 chunk 39 optimal weight: 9.9990 chunk 23 optimal weight: 8.9990 chunk 10 optimal weight: 0.9980 chunk 43 optimal weight: 8.9990 chunk 31 optimal weight: 0.8980 chunk 42 optimal weight: 20.0000 chunk 12 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.135467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.108846 restraints weight = 32580.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.108466 restraints weight = 26707.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.108413 restraints weight = 19502.324| |-----------------------------------------------------------------------------| r_work (final): 0.3934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.5034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 5266 Z= 0.232 Angle : 0.686 6.669 7520 Z= 0.369 Chirality : 0.040 0.237 874 Planarity : 0.005 0.051 662 Dihedral : 16.930 73.874 1436 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 22.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % 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: -2.61 (0.39), residues: 427 helix: -3.60 (0.80), residues: 18 sheet: -0.41 (0.39), residues: 169 loop : -2.70 (0.38), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP H 105 HIS 0.008 0.002 HIS H 35 PHE 0.018 0.002 PHE L 76 TYR 0.029 0.002 TYR L 191 ARG 0.009 0.001 ARG L 59 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.459 Fit side-chains REVERT: H 107 ASP cc_start: 0.6433 (p0) cc_final: 0.6140 (p0) REVERT: L 4 MET cc_start: 0.8515 (tmm) cc_final: 0.8187 (tmm) REVERT: L 42 LEU cc_start: 0.8665 (tp) cc_final: 0.8421 (tp) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.2068 time to fit residues: 14.9103 Evaluate side-chains 44 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 12 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 42 optimal weight: 10.0000 chunk 19 optimal weight: 20.0000 chunk 16 optimal weight: 20.0000 chunk 6 optimal weight: 2.9990 chunk 43 optimal weight: 8.9990 chunk 3 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.134870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.109429 restraints weight = 34092.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.108612 restraints weight = 26855.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.109021 restraints weight = 19840.988| |-----------------------------------------------------------------------------| r_work (final): 0.3960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.5171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 5266 Z= 0.228 Angle : 0.701 9.994 7520 Z= 0.372 Chirality : 0.040 0.220 874 Planarity : 0.005 0.048 662 Dihedral : 16.872 73.856 1436 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 23.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % 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: -2.59 (0.40), residues: 427 helix: -3.57 (0.78), residues: 18 sheet: -0.38 (0.41), residues: 169 loop : -2.70 (0.38), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP H 105 HIS 0.008 0.001 HIS H 35 PHE 0.019 0.003 PHE H 29 TYR 0.049 0.003 TYR H 27 ARG 0.008 0.001 ARG L 59 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.422 Fit side-chains REVERT: H 107 ASP cc_start: 0.6586 (p0) cc_final: 0.6257 (p0) REVERT: L 4 MET cc_start: 0.8503 (tmm) cc_final: 0.8128 (tmm) REVERT: L 42 LEU cc_start: 0.8678 (tp) cc_final: 0.8336 (tp) REVERT: L 180 MET cc_start: 0.7056 (mmm) cc_final: 0.6117 (mmm) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1585 time to fit residues: 10.8843 Evaluate side-chains 44 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 13 optimal weight: 7.9990 chunk 38 optimal weight: 10.0000 chunk 33 optimal weight: 0.0670 chunk 8 optimal weight: 0.7980 chunk 9 optimal weight: 7.9990 chunk 1 optimal weight: 20.0000 chunk 49 optimal weight: 30.0000 chunk 16 optimal weight: 0.8980 chunk 35 optimal weight: 6.9990 chunk 17 optimal weight: 9.9990 chunk 2 optimal weight: 4.9990 overall best weight: 2.7522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.135058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.104708 restraints weight = 33575.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.106759 restraints weight = 21109.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.108037 restraints weight = 15112.682| |-----------------------------------------------------------------------------| r_work (final): 0.3978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.5276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5266 Z= 0.234 Angle : 0.684 7.867 7520 Z= 0.369 Chirality : 0.040 0.208 874 Planarity : 0.005 0.050 662 Dihedral : 16.819 73.871 1436 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 23.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % 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: -2.57 (0.40), residues: 427 helix: -3.75 (0.70), residues: 18 sheet: -0.34 (0.41), residues: 169 loop : -2.70 (0.38), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP H 109 HIS 0.007 0.001 HIS H 35 PHE 0.020 0.002 PHE L 76 TYR 0.028 0.002 TYR H 27 ARG 0.009 0.001 ARG L 59 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2403.52 seconds wall clock time: 45 minutes 39.72 seconds (2739.72 seconds total)