Starting phenix.real_space_refine on Wed Oct 9 16:59:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cmh_45748/10_2024/9cmh_45748.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cmh_45748/10_2024/9cmh_45748.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cmh_45748/10_2024/9cmh_45748.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cmh_45748/10_2024/9cmh_45748.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cmh_45748/10_2024/9cmh_45748.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cmh_45748/10_2024/9cmh_45748.cif" } resolution = 4.0 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= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 18 5.16 5 C 2270 2.51 5 N 582 2.21 5 O 683 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 3553 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1324 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 4, 'TRANS': 175} Chain: "B" Number of atoms: 2229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2229 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 7, 'TRANS': 278} Time building chain proxies: 2.84, per 1000 atoms: 0.80 Number of scatterers: 3553 At special positions: 0 Unit cell: (65.994, 51.76, 148.81, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 18 16.00 O 683 8.00 N 582 7.00 C 2270 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 64 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 413.4 milliseconds 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 850 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 8 sheets defined 31.5% alpha, 25.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 5 through 27 Processing helix chain 'A' and resid 69 through 73 removed outlier: 3.928A pdb=" N ALA A 72 " --> pdb=" O SER A 69 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU A 73 " --> pdb=" O LEU A 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 69 through 73' Processing helix chain 'A' and resid 77 through 104 removed outlier: 3.593A pdb=" N CYS A 104 " --> pdb=" O VAL A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 149 Proline residue: A 135 - end of helix Processing helix chain 'A' and resid 161 through 184 Processing helix chain 'B' and resid 92 through 104 Processing helix chain 'B' and resid 170 through 174 removed outlier: 3.624A pdb=" N ILE B 174 " --> pdb=" O LEU B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 218 removed outlier: 3.788A pdb=" N ASN B 218 " --> pdb=" O ALA B 214 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 48 Processing sheet with id=AA2, first strand: chain 'B' and resid 57 through 61 removed outlier: 6.313A pdb=" N VAL B 57 " --> pdb=" O ALA B 134 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ALA B 134 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N SER B 59 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN B 61 " --> pdb=" O TYR B 130 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N LYS B 138 " --> pdb=" O LYS B 46 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE B 195 " --> pdb=" O ASP B 45 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 80 through 83 removed outlier: 4.571A pdb=" N GLY B 153 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE B 155 " --> pdb=" O TYR B 139 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR B 139 " --> pdb=" O ILE B 155 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N THR B 135 " --> pdb=" O THR B 159 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ILE B 161 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N TYR B 133 " --> pdb=" O ILE B 161 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU B 163 " --> pdb=" O LYS B 131 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N LYS B 131 " --> pdb=" O LEU B 163 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LYS B 165 " --> pdb=" O TYR B 129 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N TYR B 129 " --> pdb=" O LYS B 165 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N SER B 167 " --> pdb=" O TYR B 127 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N TYR B 127 " --> pdb=" O SER B 167 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N LYS B 138 " --> pdb=" O LYS B 46 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 50 through 51 Processing sheet with id=AA5, first strand: chain 'B' and resid 67 through 71 Processing sheet with id=AA6, first strand: chain 'B' and resid 208 through 209 removed outlier: 3.575A pdb=" N LEU B 240 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ILE B 263 " --> pdb=" O LEU B 274 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 225 through 227 Processing sheet with id=AA8, first strand: chain 'B' and resid 249 through 254 removed outlier: 3.788A pdb=" N LEU B 291 " --> pdb=" O GLN B 249 " (cutoff:3.500A) 168 hydrogen bonds defined for protein. 468 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.97 Time building geometry restraints manager: 1.01 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: 1133 1.34 - 1.46: 688 1.46 - 1.58: 1771 1.58 - 1.70: 0 1.70 - 1.81: 27 Bond restraints: 3619 Sorted by residual: bond pdb=" CB VAL A 90 " pdb=" CG1 VAL A 90 " ideal model delta sigma weight residual 1.521 1.459 0.062 3.30e-02 9.18e+02 3.58e+00 bond pdb=" CG LEU A 130 " pdb=" CD2 LEU A 130 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.95e+00 bond pdb=" CB GLN A 156 " pdb=" CG GLN A 156 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.63e+00 bond pdb=" CA MET A 22 " pdb=" CB MET A 22 " ideal model delta sigma weight residual 1.528 1.548 -0.019 1.56e-02 4.11e+03 1.55e+00 bond pdb=" CB MET A 62 " pdb=" CG MET A 62 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.47e+00 ... (remaining 3614 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.89: 4856 2.89 - 5.78: 53 5.78 - 8.68: 8 8.68 - 11.57: 5 11.57 - 14.46: 1 Bond angle restraints: 4923 Sorted by residual: angle pdb=" CB MET A 22 " pdb=" CG MET A 22 " pdb=" SD MET A 22 " ideal model delta sigma weight residual 112.70 127.16 -14.46 3.00e+00 1.11e-01 2.32e+01 angle pdb=" CA MET A 22 " pdb=" CB MET A 22 " pdb=" CG MET A 22 " ideal model delta sigma weight residual 114.10 122.94 -8.84 2.00e+00 2.50e-01 1.95e+01 angle pdb=" N MET A 22 " pdb=" CA MET A 22 " pdb=" CB MET A 22 " ideal model delta sigma weight residual 110.12 115.80 -5.68 1.47e+00 4.63e-01 1.50e+01 angle pdb=" CB MET A 62 " pdb=" CG MET A 62 " pdb=" SD MET A 62 " ideal model delta sigma weight residual 112.70 123.91 -11.21 3.00e+00 1.11e-01 1.40e+01 angle pdb=" CA GLN A 156 " pdb=" CB GLN A 156 " pdb=" CG GLN A 156 " ideal model delta sigma weight residual 114.10 121.23 -7.13 2.00e+00 2.50e-01 1.27e+01 ... (remaining 4918 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.05: 1827 14.05 - 28.10: 203 28.10 - 42.15: 70 42.15 - 56.20: 13 56.20 - 70.25: 15 Dihedral angle restraints: 2128 sinusoidal: 793 harmonic: 1335 Sorted by residual: dihedral pdb=" CA MET A 131 " pdb=" C MET A 131 " pdb=" N VAL A 132 " pdb=" CA VAL A 132 " ideal model delta harmonic sigma weight residual 180.00 160.93 19.07 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA PRO A 28 " pdb=" C PRO A 28 " pdb=" N MET A 29 " pdb=" CA MET A 29 " ideal model delta harmonic sigma weight residual 180.00 -162.19 -17.81 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA MET A 62 " pdb=" C MET A 62 " pdb=" N GLN A 63 " pdb=" CA GLN A 63 " ideal model delta harmonic sigma weight residual 180.00 162.24 17.76 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 2125 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 358 0.034 - 0.067: 145 0.067 - 0.100: 46 0.100 - 0.134: 22 0.134 - 0.167: 8 Chirality restraints: 579 Sorted by residual: chirality pdb=" CA MET A 22 " pdb=" N MET A 22 " pdb=" C MET A 22 " pdb=" CB MET A 22 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.00e-01 chirality pdb=" CB VAL B 118 " pdb=" CA VAL B 118 " pdb=" CG1 VAL B 118 " pdb=" CG2 VAL B 118 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 6.89e-01 chirality pdb=" CB VAL A 132 " pdb=" CA VAL A 132 " pdb=" CG1 VAL A 132 " pdb=" CG2 VAL A 132 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.39e-01 ... (remaining 576 not shown) Planarity restraints: 618 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 75 " -0.013 2.00e-02 2.50e+03 2.60e-02 6.77e+00 pdb=" C GLN A 75 " 0.045 2.00e-02 2.50e+03 pdb=" O GLN A 75 " -0.017 2.00e-02 2.50e+03 pdb=" N ASP A 76 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 81 " 0.009 2.00e-02 2.50e+03 1.85e-02 3.41e+00 pdb=" C VAL B 81 " -0.032 2.00e-02 2.50e+03 pdb=" O VAL B 81 " 0.012 2.00e-02 2.50e+03 pdb=" N SER B 82 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 224 " 0.010 2.00e-02 2.50e+03 1.01e-02 2.04e+00 pdb=" CG TYR B 224 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR B 224 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR B 224 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR B 224 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 224 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR B 224 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 224 " 0.000 2.00e-02 2.50e+03 ... (remaining 615 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 71 2.65 - 3.22: 3684 3.22 - 3.78: 6189 3.78 - 4.34: 8430 4.34 - 4.90: 12976 Nonbonded interactions: 31350 Sorted by model distance: nonbonded pdb=" OG SER B 60 " pdb=" OH TYR B 129 " model vdw 2.092 3.040 nonbonded pdb=" O TYR B 232 " pdb=" OH TYR B 306 " model vdw 2.106 3.040 nonbonded pdb=" NE2 GLN B 140 " pdb=" OD1 ASP B 152 " model vdw 2.162 3.120 nonbonded pdb=" O ASP B 39 " pdb=" OH TYR B 264 " model vdw 2.163 3.040 nonbonded pdb=" OG1 THR B 135 " pdb=" O THR B 159 " model vdw 2.166 3.040 ... (remaining 31345 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: 0.990 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: 0.020 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.050 Process input model: 13.010 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6602 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 0.062 3619 Z= 0.250 Angle : 0.873 14.461 4923 Z= 0.477 Chirality : 0.046 0.167 579 Planarity : 0.004 0.029 618 Dihedral : 14.789 70.254 1275 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 27.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 0.77 % Allowed : 24.81 % Favored : 74.42 % 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: -1.26 (0.39), residues: 462 helix: 1.65 (0.44), residues: 138 sheet: -2.12 (0.44), residues: 116 loop : -1.76 (0.42), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 30 HIS 0.002 0.001 HIS B 241 PHE 0.014 0.002 PHE B 268 TYR 0.025 0.002 TYR B 224 ARG 0.003 0.001 ARG B 227 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 47 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.8544 (mm) cc_final: 0.8105 (pp) REVERT: A 48 GLU cc_start: 0.6256 (tt0) cc_final: 0.5640 (tt0) REVERT: A 144 ILE cc_start: 0.6878 (mm) cc_final: 0.6590 (tt) outliers start: 3 outliers final: 3 residues processed: 49 average time/residue: 0.2515 time to fit residues: 14.7642 Evaluate side-chains 43 residues out of total 391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 40 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain B residue 247 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 38 optimal weight: 0.9980 chunk 34 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 11 optimal weight: 8.9990 chunk 23 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 36 optimal weight: 0.0060 chunk 13 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 41 optimal weight: 0.4980 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 ASN B 140 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6619 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3619 Z= 0.181 Angle : 0.614 8.442 4923 Z= 0.321 Chirality : 0.043 0.134 579 Planarity : 0.004 0.051 618 Dihedral : 5.513 52.979 500 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 22.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.79 % Allowed : 20.46 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.40), residues: 462 helix: 2.06 (0.45), residues: 138 sheet: -2.05 (0.47), residues: 113 loop : -1.84 (0.41), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 162 HIS 0.002 0.001 HIS A 141 PHE 0.012 0.001 PHE B 268 TYR 0.011 0.002 TYR B 130 ARG 0.003 0.001 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 43 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.4421 (ptt) cc_final: 0.3894 (ptt) REVERT: B 157 LYS cc_start: 0.8062 (tttt) cc_final: 0.7781 (ptmt) outliers start: 7 outliers final: 3 residues processed: 48 average time/residue: 0.1821 time to fit residues: 10.7264 Evaluate side-chains 40 residues out of total 391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 37 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 296 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 23 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 34 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 41 optimal weight: 0.3980 chunk 45 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN ** A 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 GLN B 112 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6750 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3619 Z= 0.230 Angle : 0.653 9.624 4923 Z= 0.337 Chirality : 0.045 0.287 579 Planarity : 0.004 0.040 618 Dihedral : 4.750 17.408 496 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 24.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 3.84 % Allowed : 20.97 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.39), residues: 462 helix: 2.06 (0.44), residues: 133 sheet: -2.16 (0.46), residues: 113 loop : -1.79 (0.40), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 162 HIS 0.003 0.001 HIS B 285 PHE 0.010 0.001 PHE B 104 TYR 0.008 0.002 TYR B 136 ARG 0.003 0.001 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 38 time to evaluate : 0.413 Fit side-chains revert: symmetry clash REVERT: A 16 LEU cc_start: 0.9457 (tp) cc_final: 0.9224 (tp) REVERT: A 18 TRP cc_start: 0.6259 (t60) cc_final: 0.5854 (t60) REVERT: A 19 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8358 (pp) REVERT: A 31 ARG cc_start: 0.6059 (ttm170) cc_final: 0.4818 (ttm170) REVERT: A 48 GLU cc_start: 0.6835 (tt0) cc_final: 0.6395 (tt0) REVERT: A 62 MET cc_start: 0.3006 (tpt) cc_final: 0.2567 (tmm) REVERT: A 118 MET cc_start: 0.4059 (ptt) cc_final: 0.3490 (ptt) REVERT: B 315 LEU cc_start: 0.7207 (OUTLIER) cc_final: 0.6755 (pp) outliers start: 15 outliers final: 6 residues processed: 48 average time/residue: 0.1854 time to fit residues: 10.9801 Evaluate side-chains 43 residues out of total 391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 35 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 296 TYR Chi-restraints excluded: chain B residue 315 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 21 optimal weight: 0.8980 chunk 4 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 41 optimal weight: 0.0870 chunk 44 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 0 optimal weight: 9.9990 overall best weight: 0.9360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6749 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3619 Z= 0.197 Angle : 0.644 10.469 4923 Z= 0.328 Chirality : 0.044 0.272 579 Planarity : 0.003 0.031 618 Dihedral : 4.615 16.333 496 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 22.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 3.32 % Allowed : 21.99 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.40), residues: 462 helix: 2.23 (0.45), residues: 133 sheet: -1.84 (0.49), residues: 108 loop : -1.83 (0.40), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 162 HIS 0.001 0.001 HIS B 285 PHE 0.013 0.001 PHE B 316 TYR 0.009 0.001 TYR B 156 ARG 0.003 0.001 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 40 time to evaluate : 0.429 Fit side-chains revert: symmetry clash REVERT: A 16 LEU cc_start: 0.9440 (tp) cc_final: 0.9208 (tp) REVERT: A 18 TRP cc_start: 0.6208 (t60) cc_final: 0.5821 (t60) REVERT: A 19 LEU cc_start: 0.8818 (mm) cc_final: 0.8389 (pp) REVERT: A 52 MET cc_start: 0.8912 (ppp) cc_final: 0.8481 (ppp) REVERT: A 118 MET cc_start: 0.4081 (ptt) cc_final: 0.3456 (ptt) outliers start: 13 outliers final: 8 residues processed: 50 average time/residue: 0.1825 time to fit residues: 11.5137 Evaluate side-chains 45 residues out of total 391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 37 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 296 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 33 optimal weight: 7.9990 chunk 18 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 14 optimal weight: 9.9990 chunk 40 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 241 HIS ** B 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3619 Z= 0.257 Angle : 0.662 9.624 4923 Z= 0.339 Chirality : 0.043 0.180 579 Planarity : 0.004 0.029 618 Dihedral : 4.731 17.455 496 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 23.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 5.88 % Allowed : 20.72 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.39), residues: 462 helix: 2.12 (0.45), residues: 133 sheet: -1.71 (0.52), residues: 96 loop : -1.99 (0.38), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 162 HIS 0.004 0.001 HIS B 285 PHE 0.031 0.002 PHE B 316 TYR 0.023 0.002 TYR B 224 ARG 0.003 0.001 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 35 time to evaluate : 0.374 Fit side-chains revert: symmetry clash REVERT: A 19 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8300 (tp) REVERT: A 52 MET cc_start: 0.8975 (ppp) cc_final: 0.8399 (ppp) REVERT: B 315 LEU cc_start: 0.7598 (OUTLIER) cc_final: 0.7361 (pp) outliers start: 23 outliers final: 12 residues processed: 53 average time/residue: 0.1421 time to fit residues: 9.7012 Evaluate side-chains 47 residues out of total 391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 33 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 296 TYR Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 315 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 26 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 44 optimal weight: 0.6980 chunk 36 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 chunk 23 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 chunk 25 optimal weight: 0.0070 overall best weight: 1.1002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6857 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3619 Z= 0.222 Angle : 0.637 9.349 4923 Z= 0.326 Chirality : 0.044 0.246 579 Planarity : 0.003 0.028 618 Dihedral : 4.678 17.326 496 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 22.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 4.60 % Allowed : 22.51 % Favored : 72.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.39), residues: 462 helix: 2.12 (0.45), residues: 133 sheet: -1.64 (0.52), residues: 96 loop : -1.96 (0.38), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 162 HIS 0.002 0.001 HIS B 285 PHE 0.012 0.001 PHE B 316 TYR 0.022 0.002 TYR B 224 ARG 0.003 0.001 ARG A 81 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 36 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 TRP cc_start: 0.5929 (t60) cc_final: 0.5645 (t60) REVERT: A 19 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8361 (tp) REVERT: A 52 MET cc_start: 0.8899 (ppp) cc_final: 0.8474 (ppp) REVERT: A 118 MET cc_start: 0.4395 (ptt) cc_final: 0.3826 (ptt) REVERT: B 252 ARG cc_start: 0.4748 (OUTLIER) cc_final: 0.3034 (ptm160) outliers start: 18 outliers final: 13 residues processed: 51 average time/residue: 0.1768 time to fit residues: 11.1849 Evaluate side-chains 50 residues out of total 391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 35 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 252 ARG Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 296 TYR Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 317 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 32 optimal weight: 0.4980 chunk 25 optimal weight: 0.2980 chunk 37 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 44 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 17 optimal weight: 0.0070 chunk 26 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6773 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3619 Z= 0.166 Angle : 0.650 11.355 4923 Z= 0.320 Chirality : 0.043 0.190 579 Planarity : 0.003 0.026 618 Dihedral : 4.466 16.069 496 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 19.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 4.35 % Allowed : 23.79 % Favored : 71.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.40), residues: 462 helix: 2.29 (0.45), residues: 133 sheet: -1.47 (0.52), residues: 96 loop : -1.96 (0.38), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 226 HIS 0.001 0.000 HIS B 285 PHE 0.012 0.001 PHE B 316 TYR 0.027 0.001 TYR B 224 ARG 0.005 0.001 ARG B 143 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 37 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 TRP cc_start: 0.6019 (t60) cc_final: 0.5753 (t60) REVERT: A 19 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8350 (tp) REVERT: A 118 MET cc_start: 0.4327 (ptt) cc_final: 0.3742 (ptt) REVERT: B 252 ARG cc_start: 0.4534 (OUTLIER) cc_final: 0.2917 (ptm160) outliers start: 17 outliers final: 13 residues processed: 51 average time/residue: 0.1615 time to fit residues: 10.6211 Evaluate side-chains 49 residues out of total 391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 34 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain B residue 48 ASP Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 252 ARG Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 296 TYR Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 317 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 8 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 40 optimal weight: 10.0000 chunk 42 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6817 moved from start: 0.3674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3619 Z= 0.180 Angle : 0.654 12.076 4923 Z= 0.326 Chirality : 0.043 0.182 579 Planarity : 0.003 0.024 618 Dihedral : 4.424 16.741 496 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 20.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 4.35 % Allowed : 24.04 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.40), residues: 462 helix: 2.39 (0.46), residues: 133 sheet: -1.53 (0.52), residues: 96 loop : -1.94 (0.38), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 162 HIS 0.002 0.001 HIS B 285 PHE 0.005 0.001 PHE B 316 TYR 0.022 0.001 TYR B 224 ARG 0.005 0.001 ARG B 143 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 35 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8238 (tp) REVERT: B 174 ILE cc_start: 0.3976 (OUTLIER) cc_final: 0.3743 (mm) REVERT: B 252 ARG cc_start: 0.4616 (OUTLIER) cc_final: 0.3046 (ptm160) outliers start: 17 outliers final: 12 residues processed: 49 average time/residue: 0.1832 time to fit residues: 11.4295 Evaluate side-chains 50 residues out of total 391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 35 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain B residue 48 ASP Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 252 ARG Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 296 TYR Chi-restraints excluded: chain B residue 299 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 17 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 moved from start: 0.3918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3619 Z= 0.189 Angle : 0.679 12.788 4923 Z= 0.342 Chirality : 0.043 0.249 579 Planarity : 0.003 0.024 618 Dihedral : 4.423 16.724 496 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 20.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 4.09 % Allowed : 23.53 % Favored : 72.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.39), residues: 462 helix: 2.22 (0.46), residues: 133 sheet: -1.56 (0.52), residues: 96 loop : -1.91 (0.38), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP A 18 HIS 0.002 0.001 HIS B 285 PHE 0.007 0.001 PHE B 316 TYR 0.021 0.001 TYR B 224 ARG 0.005 0.000 ARG B 143 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 37 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8347 (tp) REVERT: A 48 GLU cc_start: 0.6642 (tp30) cc_final: 0.6257 (tp30) REVERT: B 252 ARG cc_start: 0.4584 (OUTLIER) cc_final: 0.3029 (ptm160) outliers start: 16 outliers final: 12 residues processed: 50 average time/residue: 0.1522 time to fit residues: 9.6592 Evaluate side-chains 48 residues out of total 391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 34 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain B residue 48 ASP Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 252 ARG Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 299 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 45 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 38 optimal weight: 0.0070 chunk 11 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 chunk 5 optimal weight: 0.8980 chunk 10 optimal weight: 6.9990 overall best weight: 0.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6823 moved from start: 0.4087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3619 Z= 0.188 Angle : 0.697 12.758 4923 Z= 0.344 Chirality : 0.043 0.143 579 Planarity : 0.003 0.025 618 Dihedral : 4.476 16.820 496 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 20.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 4.09 % Allowed : 24.55 % Favored : 71.36 % 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: -0.92 (0.39), residues: 462 helix: 2.13 (0.45), residues: 133 sheet: -1.51 (0.52), residues: 98 loop : -1.92 (0.38), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 18 HIS 0.002 0.001 HIS B 285 PHE 0.006 0.001 PHE B 316 TYR 0.022 0.001 TYR B 224 ARG 0.004 0.000 ARG B 143 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 35 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8151 (tp) REVERT: A 48 GLU cc_start: 0.6481 (tp30) cc_final: 0.6157 (tp30) REVERT: B 252 ARG cc_start: 0.4581 (OUTLIER) cc_final: 0.3040 (ptm160) outliers start: 16 outliers final: 14 residues processed: 49 average time/residue: 0.1702 time to fit residues: 10.4291 Evaluate side-chains 50 residues out of total 391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 34 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 53 ASN Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain B residue 48 ASP Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 252 ARG Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 299 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 36 optimal weight: 9.9990 chunk 15 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 6 optimal weight: 0.0010 chunk 32 optimal weight: 0.3980 chunk 2 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 31 optimal weight: 8.9990 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 285 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 = 0.4137 r_free = 0.4137 target = 0.086169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.075031 restraints weight = 22651.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.076666 restraints weight = 13947.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.077645 restraints weight = 9853.014| |-----------------------------------------------------------------------------| r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6800 moved from start: 0.4237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 3619 Z= 0.178 Angle : 0.733 13.153 4923 Z= 0.356 Chirality : 0.043 0.149 579 Planarity : 0.003 0.025 618 Dihedral : 4.410 16.986 496 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 19.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.84 % Allowed : 24.81 % Favored : 71.36 % 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: -0.93 (0.39), residues: 462 helix: 2.05 (0.46), residues: 133 sheet: -1.47 (0.52), residues: 98 loop : -1.90 (0.37), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 18 HIS 0.001 0.001 HIS B 146 PHE 0.007 0.001 PHE B 316 TYR 0.022 0.001 TYR B 224 ARG 0.004 0.000 ARG B 143 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1216.69 seconds wall clock time: 23 minutes 53.06 seconds (1433.06 seconds total)