Starting phenix.real_space_refine on Fri Jul 19 00:25:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xlt_33286/07_2024/7xlt_33286.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xlt_33286/07_2024/7xlt_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xlt_33286/07_2024/7xlt_33286.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xlt_33286/07_2024/7xlt_33286.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xlt_33286/07_2024/7xlt_33286.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xlt_33286/07_2024/7xlt_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 Residue "H ASP 73": "OD1" <-> "OD2" Residue "H ASP 107": "OD1" <-> "OD2" Residue "H TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 39": "OE1" <-> "OE2" Residue "L TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 75": "OD1" <-> "OD2" Residue "L PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 148": "OD1" <-> "OD2" Residue "L GLU 200": "OE1" <-> "OE2" Residue "L PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 4.01, per 1000 atoms: 0.80 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 - 3.50 Amino acid : False - 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: 2.43 Conformation dependent library (CDL) restraints added in 711.1 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: 2.24 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: 1.59 Time building geometry restraints manager: 2.62 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: 97.00 - 104.51: 392 104.51 - 112.02: 2702 112.02 - 119.54: 1788 119.54 - 127.05: 2408 127.05 - 134.56: 230 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 2.440 nonbonded pdb=" OG SER H 141 " pdb=" O VAL H 189 " model vdw 2.326 2.440 nonbonded pdb=" OG SER L 57 " pdb=" O GLY L 69 " model vdw 2.337 2.440 nonbonded pdb=" OG SER L 25 " pdb=" O GLN L 27 " model vdw 2.353 2.440 nonbonded pdb=" NH1 ARG L 66 " pdb=" OE2 GLU L 84 " model vdw 2.369 2.520 ... (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 ========== 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: 1.090 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: 0.130 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 20.750 Find NCS groups from input model: 0.050 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.030 ------------------------------------------------------------------------------- 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 fitting. 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: 0.1833 time to fit residues: 16.3926 Evaluate side-chains 62 residues out of total 379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 61 time to evaluate : 0.387 ------------------------------------------------------------------------------- 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: 5.9990 chunk 25 optimal weight: 5.9990 chunk 20 optimal weight: 0.5980 chunk 39 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 45 optimal weight: 10.0000 overall best weight: 4.5188 ------------------------------------------------------------------------------- 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 ** L 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6318 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 5266 Z= 0.337 Angle : 0.756 8.718 7520 Z= 0.405 Chirality : 0.039 0.155 874 Planarity : 0.006 0.067 662 Dihedral : 16.611 73.951 1436 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 27.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.13 % Favored : 90.87 % Rotamer: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % 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: -2.39 (0.38), residues: 427 helix: -3.26 (0.93), residues: 18 sheet: -0.34 (0.38), residues: 179 loop : -2.59 (0.37), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP H 109 HIS 0.008 0.002 HIS H 205 PHE 0.024 0.003 PHE L 76 TYR 0.017 0.002 TYR L 41 ARG 0.003 0.001 ARG L 113 *********************** 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 65 residues out of total 379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.399 Fit side-chains revert: symmetry clash REVERT: H 20 MET cc_start: 0.7688 (tpp) cc_final: 0.7251 (tpt) REVERT: H 45 LEU cc_start: 0.7966 (mt) cc_final: 0.7619 (mt) REVERT: L 78 LEU cc_start: 0.7911 (tt) cc_final: 0.7649 (tt) REVERT: L 92 TYR cc_start: 0.6851 (m-10) cc_final: 0.6475 (m-10) REVERT: L 102 THR cc_start: 0.7274 (m) cc_final: 0.6931 (m) REVERT: L 103 PHE cc_start: 0.8081 (t80) cc_final: 0.7678 (t80) REVERT: L 144 PHE cc_start: 0.6469 (m-10) cc_final: 0.6124 (m-10) REVERT: L 149 ILE cc_start: 0.6756 (mm) cc_final: 0.6465 (mm) REVERT: L 180 MET cc_start: 0.7625 (mmm) cc_final: 0.7289 (mmm) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.1578 time to fit residues: 13.3696 Evaluate side-chains 47 residues out of total 379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 45 optimal weight: 10.0000 chunk 49 optimal weight: 30.0000 chunk 40 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 36 optimal weight: 30.0000 chunk 44 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 39 GLN ** H 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6361 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5266 Z= 0.244 Angle : 0.694 7.680 7520 Z= 0.371 Chirality : 0.038 0.156 874 Planarity : 0.005 0.053 662 Dihedral : 16.715 73.929 1436 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 24.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % 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: -2.33 (0.38), residues: 427 helix: -2.76 (0.93), residues: 18 sheet: -0.17 (0.39), residues: 169 loop : -2.61 (0.35), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 47 HIS 0.006 0.002 HIS H 35 PHE 0.014 0.002 PHE L 140 TYR 0.014 0.002 TYR H 54 ARG 0.002 0.001 ARG L 113 *********************** 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 55 residues out of total 379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.593 Fit side-chains revert: symmetry clash REVERT: L 92 TYR cc_start: 0.6751 (m-10) cc_final: 0.6441 (m-10) REVERT: L 103 PHE cc_start: 0.7981 (t80) cc_final: 0.7637 (t80) REVERT: L 144 PHE cc_start: 0.6450 (m-10) cc_final: 0.6110 (m-10) REVERT: L 149 ILE cc_start: 0.6560 (mm) cc_final: 0.6216 (mm) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1741 time to fit residues: 12.6300 Evaluate side-chains 46 residues out of total 379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 34 optimal weight: 40.0000 chunk 23 optimal weight: 0.0070 chunk 5 optimal weight: 6.9990 chunk 21 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 45 optimal weight: 10.0000 chunk 48 optimal weight: 9.9990 chunk 43 optimal weight: 7.9990 chunk 13 optimal weight: 0.4980 chunk 40 optimal weight: 9.9990 chunk 27 optimal weight: 7.9990 overall best weight: 2.4602 ------------------------------------------------------------------------------- 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** ** L 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6347 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5266 Z= 0.220 Angle : 0.659 8.810 7520 Z= 0.351 Chirality : 0.037 0.152 874 Planarity : 0.005 0.042 662 Dihedral : 16.681 73.848 1436 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 24.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % 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: -2.28 (1.11), residues: 18 sheet: -0.10 (0.40), residues: 171 loop : -2.56 (0.36), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 109 HIS 0.004 0.001 HIS H 35 PHE 0.017 0.002 PHE L 76 TYR 0.011 0.001 TYR L 91 ARG 0.002 0.001 ARG H 104 *********************** 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 55 residues out of total 379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.426 Fit side-chains revert: symmetry clash REVERT: L 92 TYR cc_start: 0.6855 (m-10) cc_final: 0.6493 (m-10) REVERT: L 144 PHE cc_start: 0.6474 (m-10) cc_final: 0.6184 (m-10) REVERT: L 149 ILE cc_start: 0.6597 (mm) cc_final: 0.6173 (mm) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1647 time to fit residues: 11.8091 Evaluate side-chains 47 residues out of total 379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 19 optimal weight: 20.0000 chunk 41 optimal weight: 4.9990 chunk 33 optimal weight: 0.0060 chunk 24 optimal weight: 20.0000 chunk 43 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 16 optimal weight: 0.0980 chunk 9 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 overall best weight: 3.2202 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6425 moved from start: 0.4011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5266 Z= 0.253 Angle : 0.683 6.856 7520 Z= 0.367 Chirality : 0.038 0.156 874 Planarity : 0.005 0.043 662 Dihedral : 16.764 73.936 1436 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 27.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % 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: -2.33 (0.39), residues: 427 helix: -2.86 (0.96), residues: 18 sheet: -0.24 (0.40), residues: 169 loop : -2.54 (0.36), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP H 36 HIS 0.002 0.001 HIS L 31 PHE 0.015 0.002 PHE L 76 TYR 0.014 0.002 TYR L 91 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 56 residues out of total 379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.465 Fit side-chains revert: symmetry clash REVERT: H 36 TRP cc_start: 0.6320 (m100) cc_final: 0.5752 (m100) REVERT: L 92 TYR cc_start: 0.6914 (m-80) cc_final: 0.6421 (m-10) REVERT: L 103 PHE cc_start: 0.8099 (t80) cc_final: 0.7821 (t80) REVERT: L 144 PHE cc_start: 0.6487 (m-10) cc_final: 0.6003 (m-10) REVERT: L 149 ILE cc_start: 0.6760 (mm) cc_final: 0.6309 (mm) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.1735 time to fit residues: 12.7297 Evaluate side-chains 48 residues out of total 379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 9.9990 chunk 48 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 22 optimal weight: 8.9990 chunk 4 optimal weight: 4.9990 chunk 16 optimal weight: 20.0000 chunk 25 optimal weight: 5.9990 chunk 46 optimal weight: 30.0000 chunk 5 optimal weight: 0.3980 chunk 27 optimal weight: 9.9990 chunk 35 optimal weight: 8.9990 overall best weight: 5.4788 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6588 moved from start: 0.4697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 5266 Z= 0.376 Angle : 0.795 7.985 7520 Z= 0.424 Chirality : 0.042 0.243 874 Planarity : 0.006 0.062 662 Dihedral : 17.067 74.266 1436 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 36.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.54 % Favored : 89.46 % Rotamer: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % 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: -2.63 (0.38), residues: 427 helix: -2.34 (1.19), residues: 18 sheet: -0.56 (0.38), residues: 171 loop : -2.72 (0.37), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.004 TRP H 109 HIS 0.006 0.002 HIS H 35 PHE 0.022 0.003 PHE H 106 TYR 0.020 0.002 TYR L 41 ARG 0.006 0.001 ARG L 59 *********************** 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 54 residues out of total 379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.416 Fit side-chains REVERT: H 20 MET cc_start: 0.7656 (tpp) cc_final: 0.7210 (tpt) REVERT: L 144 PHE cc_start: 0.6587 (m-10) cc_final: 0.6185 (m-10) REVERT: L 149 ILE cc_start: 0.6859 (mm) cc_final: 0.6458 (mm) REVERT: L 180 MET cc_start: 0.7637 (mmm) cc_final: 0.7372 (mmm) REVERT: L 192 GLU cc_start: 0.6824 (mp0) cc_final: 0.5700 (tp30) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.1539 time to fit residues: 11.0446 Evaluate side-chains 47 residues out of total 379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 8.9990 chunk 40 optimal weight: 5.9990 chunk 48 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 22 optimal weight: 4.9990 chunk 19 optimal weight: 20.0000 chunk 28 optimal weight: 6.9990 chunk 14 optimal weight: 20.0000 chunk 9 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- 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 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6534 moved from start: 0.4811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 5266 Z= 0.285 Angle : 0.722 7.376 7520 Z= 0.389 Chirality : 0.040 0.209 874 Planarity : 0.005 0.042 662 Dihedral : 17.091 74.062 1436 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 31.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.37 % Favored : 90.63 % Rotamer: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % 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 (0.39), residues: 427 helix: -2.55 (1.14), residues: 18 sheet: -0.49 (0.38), residues: 173 loop : -2.73 (0.37), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP H 109 HIS 0.008 0.001 HIS H 35 PHE 0.021 0.003 PHE H 106 TYR 0.020 0.002 TYR H 27 ARG 0.006 0.001 ARG H 98 *********************** 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 57 residues out of total 379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.444 Fit side-chains REVERT: H 107 ASP cc_start: 0.6363 (p0) cc_final: 0.5103 (p0) REVERT: L 144 PHE cc_start: 0.6690 (m-10) cc_final: 0.6366 (m-10) REVERT: L 149 ILE cc_start: 0.6743 (mm) cc_final: 0.6271 (mm) REVERT: L 192 GLU cc_start: 0.6954 (mp0) cc_final: 0.5712 (tp30) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.1848 time to fit residues: 13.6790 Evaluate side-chains 47 residues out of total 379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 20.0000 chunk 4 optimal weight: 0.7980 chunk 37 optimal weight: 5.9990 chunk 43 optimal weight: 8.9990 chunk 46 optimal weight: 30.0000 chunk 42 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 27 optimal weight: 8.9990 chunk 19 optimal weight: 3.9990 chunk 35 optimal weight: 9.9990 chunk 13 optimal weight: 30.0000 overall best weight: 5.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN ** H 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6674 moved from start: 0.5600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 5266 Z= 0.388 Angle : 0.838 8.047 7520 Z= 0.446 Chirality : 0.044 0.204 874 Planarity : 0.006 0.073 662 Dihedral : 17.425 74.318 1436 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 39.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.88 % Favored : 87.12 % Rotamer: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % 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: -2.89 (0.39), residues: 427 helix: -2.95 (0.99), residues: 18 sheet: -0.68 (0.40), residues: 166 loop : -2.88 (0.37), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.004 TRP H 47 HIS 0.009 0.002 HIS H 35 PHE 0.029 0.003 PHE L 76 TYR 0.020 0.003 TYR H 27 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 fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.451 Fit side-chains REVERT: L 144 PHE cc_start: 0.6744 (m-10) cc_final: 0.6468 (m-10) REVERT: L 149 ILE cc_start: 0.6896 (mm) cc_final: 0.6370 (mm) REVERT: L 192 GLU cc_start: 0.6909 (mp0) cc_final: 0.5743 (tp30) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.1560 time to fit residues: 11.0947 Evaluate side-chains 43 residues out of total 379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 29 optimal weight: 0.0000 chunk 47 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 22 optimal weight: 8.9990 chunk 33 optimal weight: 0.0000 chunk 49 optimal weight: 30.0000 chunk 45 optimal weight: 20.0000 chunk 39 optimal weight: 0.8980 overall best weight: 2.7792 ------------------------------------------------------------------------------- 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 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6504 moved from start: 0.5398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5266 Z= 0.236 Angle : 0.708 8.157 7520 Z= 0.379 Chirality : 0.039 0.191 874 Planarity : 0.005 0.042 662 Dihedral : 17.181 73.964 1436 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 27.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % 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: -2.62 (0.39), residues: 427 helix: -2.96 (0.99), residues: 18 sheet: -0.41 (0.39), residues: 168 loop : -2.77 (0.38), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP H 47 HIS 0.009 0.002 HIS H 35 PHE 0.017 0.002 PHE L 76 TYR 0.017 0.002 TYR H 27 ARG 0.003 0.001 ARG H 104 *********************** 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 56 residues out of total 379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.444 Fit side-chains REVERT: L 192 GLU cc_start: 0.6741 (mp0) cc_final: 0.5411 (tp30) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.1509 time to fit residues: 11.3073 Evaluate side-chains 45 residues out of total 379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 0.8980 chunk 30 optimal weight: 7.9990 chunk 24 optimal weight: 8.9990 chunk 31 optimal weight: 1.9990 chunk 42 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 36 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 11 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 chunk 16 optimal weight: 20.0000 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 171 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6483 moved from start: 0.5428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5266 Z= 0.221 Angle : 0.700 10.425 7520 Z= 0.370 Chirality : 0.039 0.180 874 Planarity : 0.005 0.041 662 Dihedral : 16.999 73.882 1436 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 26.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.13 % Favored : 90.87 % 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 (0.39), residues: 427 helix: -2.91 (0.92), residues: 18 sheet: -0.42 (0.40), residues: 166 loop : -2.69 (0.38), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP H 47 HIS 0.006 0.001 HIS H 35 PHE 0.012 0.002 PHE H 106 TYR 0.032 0.002 TYR L 191 ARG 0.003 0.001 ARG L 24 ********************** 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 54 residues out of total 379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.387 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.1448 time to fit residues: 10.4384 Evaluate side-chains 45 residues out of total 379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 7 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 45 optimal weight: 20.0000 chunk 26 optimal weight: 1.9990 chunk 1 optimal weight: 9.9990 chunk 31 optimal weight: 0.0980 chunk 30 optimal weight: 0.8980 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 171 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.134801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.104411 restraints weight = 32909.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.106419 restraints weight = 21019.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.107462 restraints weight = 15104.304| |-----------------------------------------------------------------------------| r_work (final): 0.3970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.5491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5266 Z= 0.213 Angle : 0.682 10.162 7520 Z= 0.363 Chirality : 0.038 0.186 874 Planarity : 0.005 0.041 662 Dihedral : 16.830 73.835 1436 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 24.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % 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: -2.41 (0.40), residues: 427 helix: -2.83 (0.93), residues: 18 sheet: -0.30 (0.40), residues: 167 loop : -2.59 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP H 109 HIS 0.008 0.002 HIS H 35 PHE 0.011 0.002 PHE L 76 TYR 0.031 0.002 TYR L 191 ARG 0.004 0.001 ARG L 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1159.75 seconds wall clock time: 21 minutes 46.39 seconds (1306.39 seconds total)