Starting phenix.real_space_refine on Fri Apr 5 12:03:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p36_17384/04_2024/8p36_17384_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p36_17384/04_2024/8p36_17384.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p36_17384/04_2024/8p36_17384.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p36_17384/04_2024/8p36_17384.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p36_17384/04_2024/8p36_17384_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p36_17384/04_2024/8p36_17384_updated.pdb" } resolution = 2.51 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= 0.027 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 1 5.49 5 S 4 5.16 5 C 760 2.51 5 N 209 2.21 5 O 249 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 1223 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1197 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 156} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {'B6D': 1, 'G3P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.26, per 1000 atoms: 1.03 Number of scatterers: 1223 At special positions: 0 Unit cell: (45.57, 45.57, 96.72, 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 4 16.00 P 1 15.00 O 249 8.00 N 209 7.00 C 760 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 120 " - pdb=" SG CYS A 154 " distance=2.03 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.63 Conformation dependent library (CDL) restraints added in 226.2 milliseconds 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 302 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 6 helices and 1 sheets defined 36.6% alpha, 14.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 3 through 17 Processing helix chain 'A' and resid 24 through 54 removed outlier: 3.795A pdb=" N GLU A 35 " --> pdb=" O ALA A 31 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA A 36 " --> pdb=" O GLN A 32 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLN A 43 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N SER A 45 " --> pdb=" O GLU A 41 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ALA A 46 " --> pdb=" O GLY A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 64 No H-bonds generated for 'chain 'A' and resid 61 through 64' Processing helix chain 'A' and resid 98 through 100 No H-bonds generated for 'chain 'A' and resid 98 through 100' Processing helix chain 'A' and resid 147 through 149 No H-bonds generated for 'chain 'A' and resid 147 through 149' Processing helix chain 'A' and resid 152 through 154 No H-bonds generated for 'chain 'A' and resid 152 through 154' Processing sheet with id= A, first strand: chain 'A' and resid 116 through 122 48 hydrogen bonds defined for protein. 141 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: 0.28 Time building geometry restraints manager: 0.66 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: 402 1.34 - 1.45: 146 1.45 - 1.57: 685 1.57 - 1.69: 1 1.69 - 1.80: 6 Bond restraints: 1240 Sorted by residual: bond pdb=" O1P G3P A 201 " pdb=" P G3P A 201 " ideal model delta sigma weight residual 1.726 1.608 0.118 2.00e-02 2.50e+03 3.49e+01 bond pdb=" C3 B6D A 202 " pdb=" O3 B6D A 202 " ideal model delta sigma weight residual 1.404 1.433 -0.029 2.00e-02 2.50e+03 2.08e+00 bond pdb=" CA ILE A 72 " pdb=" CB ILE A 72 " ideal model delta sigma weight residual 1.540 1.524 0.016 1.36e-02 5.41e+03 1.32e+00 bond pdb=" C1 B6D A 202 " pdb=" O5 B6D A 202 " ideal model delta sigma weight residual 1.405 1.427 -0.022 2.00e-02 2.50e+03 1.17e+00 bond pdb=" O3P G3P A 201 " pdb=" P G3P A 201 " ideal model delta sigma weight residual 1.526 1.507 0.019 2.00e-02 2.50e+03 9.19e-01 ... (remaining 1235 not shown) Histogram of bond angle deviations from ideal: 98.23 - 105.38: 13 105.38 - 112.53: 695 112.53 - 119.69: 384 119.69 - 126.84: 581 126.84 - 134.00: 15 Bond angle restraints: 1688 Sorted by residual: angle pdb=" O1P G3P A 201 " pdb=" P G3P A 201 " pdb=" O4P G3P A 201 " ideal model delta sigma weight residual 100.65 109.77 -9.12 3.00e+00 1.11e-01 9.24e+00 angle pdb=" N GLY A 121 " pdb=" CA GLY A 121 " pdb=" C GLY A 121 " ideal model delta sigma weight residual 111.42 114.92 -3.50 1.51e+00 4.39e-01 5.39e+00 angle pdb=" O2P G3P A 201 " pdb=" P G3P A 201 " pdb=" O4P G3P A 201 " ideal model delta sigma weight residual 115.71 109.88 5.83 3.00e+00 1.11e-01 3.78e+00 angle pdb=" O1P G3P A 201 " pdb=" P G3P A 201 " pdb=" O3P G3P A 201 " ideal model delta sigma weight residual 104.20 109.93 -5.73 3.00e+00 1.11e-01 3.65e+00 angle pdb=" O3P G3P A 201 " pdb=" P G3P A 201 " pdb=" O4P G3P A 201 " ideal model delta sigma weight residual 115.20 109.53 5.67 3.00e+00 1.11e-01 3.57e+00 ... (remaining 1683 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 16.09: 638 16.09 - 32.17: 77 32.17 - 48.25: 27 48.25 - 64.33: 15 64.33 - 80.41: 3 Dihedral angle restraints: 760 sinusoidal: 293 harmonic: 467 Sorted by residual: dihedral pdb=" CG ARG A 126 " pdb=" CD ARG A 126 " pdb=" NE ARG A 126 " pdb=" CZ ARG A 126 " ideal model delta sinusoidal sigma weight residual 180.00 135.42 44.58 2 1.50e+01 4.44e-03 1.05e+01 dihedral pdb=" CB LYS A 73 " pdb=" CG LYS A 73 " pdb=" CD LYS A 73 " pdb=" CE LYS A 73 " ideal model delta sinusoidal sigma weight residual 60.00 118.13 -58.13 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" CA GLU A 41 " pdb=" CB GLU A 41 " pdb=" CG GLU A 41 " pdb=" CD GLU A 41 " ideal model delta sinusoidal sigma weight residual -60.00 -115.07 55.07 3 1.50e+01 4.44e-03 9.32e+00 ... (remaining 757 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.042: 151 0.042 - 0.083: 40 0.083 - 0.125: 12 0.125 - 0.166: 0 0.166 - 0.207: 1 Chirality restraints: 204 Sorted by residual: chirality pdb=" C4 B6D A 202 " pdb=" C3 B6D A 202 " pdb=" C5 B6D A 202 " pdb=" N4 B6D A 202 " both_signs ideal model delta sigma weight residual False -2.31 -2.52 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA VAL A 82 " pdb=" N VAL A 82 " pdb=" C VAL A 82 " pdb=" CB VAL A 82 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.22e-01 chirality pdb=" CA VAL A 80 " pdb=" N VAL A 80 " pdb=" C VAL A 80 " pdb=" CB VAL A 80 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.18e-01 ... (remaining 201 not shown) Planarity restraints: 213 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 B6D A 202 " -0.019 2.00e-02 2.50e+03 1.57e-02 3.09e+00 pdb=" C7 B6D A 202 " 0.005 2.00e-02 2.50e+03 pdb=" C8 B6D A 202 " -0.015 2.00e-02 2.50e+03 pdb=" N2 B6D A 202 " 0.025 2.00e-02 2.50e+03 pdb=" O7 B6D A 202 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 122 " -0.019 5.00e-02 4.00e+02 2.82e-02 1.27e+00 pdb=" N PRO A 123 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO A 123 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 123 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 21 " 0.012 5.00e-02 4.00e+02 1.85e-02 5.48e-01 pdb=" N PRO A 22 " -0.032 5.00e-02 4.00e+02 pdb=" CA PRO A 22 " 0.009 5.00e-02 4.00e+02 pdb=" CD PRO A 22 " 0.010 5.00e-02 4.00e+02 ... (remaining 210 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 119 2.74 - 3.28: 1177 3.28 - 3.82: 2113 3.82 - 4.36: 2483 4.36 - 4.90: 4249 Nonbonded interactions: 10141 Sorted by model distance: nonbonded pdb=" O1 G3P A 201 " pdb=" O1P G3P A 201 " model vdw 2.195 2.440 nonbonded pdb=" O LYS A 44 " pdb=" OG1 THR A 48 " model vdw 2.285 2.440 nonbonded pdb=" NZ LYS A 110 " pdb=" O ALA A 160 " model vdw 2.379 2.520 nonbonded pdb=" NZ LYS A 140 " pdb=" OD2 ASP A 143 " model vdw 2.425 2.520 nonbonded pdb=" O LEU A 39 " pdb=" NE2 GLN A 43 " model vdw 2.453 2.520 ... (remaining 10136 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.850 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.140 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 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 : 0.005 0.118 1240 Z= 0.354 Angle : 0.633 9.119 1688 Z= 0.291 Chirality : 0.042 0.207 204 Planarity : 0.003 0.028 213 Dihedral : 18.623 80.410 455 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 5.51 % Allowed : 29.92 % Favored : 64.57 % 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 (0.68), residues: 159 helix: 1.85 (0.71), residues: 49 sheet: -1.23 (0.95), residues: 24 loop : 0.92 (0.74), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 108 HIS 0.001 0.001 HIS A 54 PHE 0.005 0.001 PHE A 119 TYR 0.006 0.001 TYR A 50 ARG 0.001 0.000 ARG A 30 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 24 time to evaluate : 0.144 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 30 average time/residue: 0.6971 time to fit residues: 21.4450 Evaluate side-chains 25 residues out of total 128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 19 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 154 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 13 optimal weight: 8.9990 chunk 12 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 1240 Z= 0.204 Angle : 0.478 6.221 1688 Z= 0.244 Chirality : 0.040 0.119 204 Planarity : 0.003 0.025 213 Dihedral : 5.466 45.999 202 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.72 % Allowed : 27.56 % Favored : 67.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.69), residues: 159 helix: 1.39 (0.67), residues: 55 sheet: -0.92 (1.00), residues: 26 loop : 0.79 (0.78), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 108 HIS 0.001 0.001 HIS A 54 PHE 0.001 0.000 PHE A 119 TYR 0.008 0.001 TYR A 50 ARG 0.001 0.000 ARG A 30 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 23 time to evaluate : 0.142 Fit side-chains REVERT: A 5 GLU cc_start: 0.6762 (OUTLIER) cc_final: 0.6368 (tp30) outliers start: 6 outliers final: 1 residues processed: 27 average time/residue: 0.6475 time to fit residues: 17.9739 Evaluate side-chains 25 residues out of total 128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 23 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLU Chi-restraints excluded: chain A residue 154 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 7 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 8 optimal weight: 6.9990 chunk 0 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN A 98 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 1240 Z= 0.201 Angle : 0.457 4.368 1688 Z= 0.239 Chirality : 0.041 0.116 204 Planarity : 0.002 0.022 213 Dihedral : 5.081 47.838 197 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.36 % Allowed : 29.13 % Favored : 68.50 % 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: 1.05 (0.69), residues: 159 helix: 1.45 (0.66), residues: 55 sheet: -0.75 (1.13), residues: 24 loop : 0.83 (0.77), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 108 HIS 0.001 0.001 HIS A 149 PHE 0.002 0.000 PHE A 119 TYR 0.008 0.001 TYR A 50 ARG 0.001 0.000 ARG A 30 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 26 time to evaluate : 0.158 Fit side-chains REVERT: A 5 GLU cc_start: 0.6651 (OUTLIER) cc_final: 0.6277 (tp30) outliers start: 3 outliers final: 2 residues processed: 28 average time/residue: 0.6716 time to fit residues: 19.3309 Evaluate side-chains 28 residues out of total 128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 25 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 154 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 11 optimal weight: 0.9980 chunk 6 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 chunk 12 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 1240 Z= 0.168 Angle : 0.466 7.044 1688 Z= 0.235 Chirality : 0.040 0.116 204 Planarity : 0.002 0.022 213 Dihedral : 5.015 48.101 197 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.36 % Allowed : 30.71 % Favored : 66.93 % 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 (0.69), residues: 159 helix: 1.53 (0.66), residues: 55 sheet: -0.83 (1.00), residues: 26 loop : 0.82 (0.79), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 108 HIS 0.001 0.001 HIS A 54 PHE 0.001 0.000 PHE A 119 TYR 0.007 0.001 TYR A 50 ARG 0.001 0.000 ARG A 30 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 27 time to evaluate : 0.146 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 28 average time/residue: 0.6831 time to fit residues: 19.6557 Evaluate side-chains 28 residues out of total 128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 26 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 154 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 7 optimal weight: 5.9990 chunk 1 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 1240 Z= 0.255 Angle : 0.508 7.767 1688 Z= 0.254 Chirality : 0.042 0.117 204 Planarity : 0.002 0.021 213 Dihedral : 5.289 48.566 197 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.36 % Allowed : 31.50 % Favored : 66.14 % 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: 0.96 (0.69), residues: 159 helix: 1.42 (0.65), residues: 55 sheet: -0.86 (1.00), residues: 26 loop : 0.81 (0.79), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 108 HIS 0.001 0.001 HIS A 54 PHE 0.001 0.000 PHE A 119 TYR 0.008 0.001 TYR A 50 ARG 0.002 0.000 ARG A 30 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 26 time to evaluate : 0.137 Fit side-chains REVERT: A 5 GLU cc_start: 0.6755 (OUTLIER) cc_final: 0.6229 (tp30) outliers start: 3 outliers final: 2 residues processed: 27 average time/residue: 0.6891 time to fit residues: 19.0850 Evaluate side-chains 29 residues out of total 128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 26 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 154 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 3 optimal weight: 1.9990 chunk 2 optimal weight: 7.9990 chunk 9 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 1240 Z= 0.169 Angle : 0.477 7.811 1688 Z= 0.238 Chirality : 0.040 0.117 204 Planarity : 0.002 0.020 213 Dihedral : 5.000 48.327 197 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.36 % Allowed : 32.28 % Favored : 65.35 % 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: 1.01 (0.69), residues: 159 helix: 1.54 (0.66), residues: 55 sheet: -0.92 (0.98), residues: 26 loop : 0.82 (0.80), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 108 HIS 0.001 0.001 HIS A 54 PHE 0.001 0.000 PHE A 1 TYR 0.007 0.001 TYR A 50 ARG 0.001 0.000 ARG A 30 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 27 time to evaluate : 0.128 Fit side-chains REVERT: A 5 GLU cc_start: 0.6725 (OUTLIER) cc_final: 0.6232 (tp30) outliers start: 3 outliers final: 2 residues processed: 28 average time/residue: 0.6687 time to fit residues: 19.2155 Evaluate side-chains 29 residues out of total 128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 26 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 154 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 11 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 12 optimal weight: 0.0270 chunk 13 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 1240 Z= 0.151 Angle : 0.467 8.021 1688 Z= 0.232 Chirality : 0.040 0.118 204 Planarity : 0.002 0.021 213 Dihedral : 4.892 48.103 197 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.36 % Allowed : 30.71 % Favored : 66.93 % 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: 1.06 (0.69), residues: 159 helix: 1.63 (0.66), residues: 55 sheet: -0.95 (0.98), residues: 26 loop : 0.83 (0.80), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 108 HIS 0.001 0.000 HIS A 149 PHE 0.001 0.000 PHE A 1 TYR 0.006 0.001 TYR A 50 ARG 0.001 0.000 ARG A 30 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 27 time to evaluate : 0.107 Fit side-chains REVERT: A 5 GLU cc_start: 0.6711 (OUTLIER) cc_final: 0.6320 (tp30) outliers start: 3 outliers final: 2 residues processed: 28 average time/residue: 0.5283 time to fit residues: 15.1782 Evaluate side-chains 30 residues out of total 128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 27 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 154 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 11 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 2 optimal weight: 0.0980 chunk 0 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 1240 Z= 0.183 Angle : 0.480 8.261 1688 Z= 0.237 Chirality : 0.040 0.117 204 Planarity : 0.002 0.021 213 Dihedral : 4.979 48.418 197 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.15 % Allowed : 30.71 % Favored : 66.14 % 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 (0.69), residues: 159 helix: 1.52 (0.66), residues: 55 sheet: -0.96 (0.98), residues: 26 loop : 0.84 (0.80), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 108 HIS 0.001 0.001 HIS A 54 PHE 0.001 0.000 PHE A 1 TYR 0.007 0.001 TYR A 50 ARG 0.001 0.000 ARG A 30 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 27 time to evaluate : 0.115 Fit side-chains REVERT: A 5 GLU cc_start: 0.6740 (OUTLIER) cc_final: 0.6246 (tp30) outliers start: 4 outliers final: 2 residues processed: 29 average time/residue: 0.6337 time to fit residues: 18.8818 Evaluate side-chains 30 residues out of total 128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 27 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 154 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 10 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 6 optimal weight: 6.9990 chunk 5 optimal weight: 0.5980 chunk 15 optimal weight: 4.9990 chunk 2 optimal weight: 0.0060 chunk 1 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 overall best weight: 0.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 1240 Z= 0.149 Angle : 0.467 8.228 1688 Z= 0.231 Chirality : 0.040 0.118 204 Planarity : 0.002 0.021 213 Dihedral : 4.828 48.123 197 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.36 % Allowed : 31.50 % Favored : 66.14 % 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: 1.06 (0.69), residues: 159 helix: 1.63 (0.66), residues: 55 sheet: -0.93 (0.99), residues: 26 loop : 0.82 (0.80), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 108 HIS 0.001 0.000 HIS A 149 PHE 0.001 0.000 PHE A 1 TYR 0.006 0.001 TYR A 50 ARG 0.001 0.000 ARG A 30 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 26 time to evaluate : 0.120 Fit side-chains REVERT: A 5 GLU cc_start: 0.6715 (OUTLIER) cc_final: 0.6309 (tp30) outliers start: 3 outliers final: 2 residues processed: 27 average time/residue: 0.6793 time to fit residues: 18.8324 Evaluate side-chains 28 residues out of total 128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 25 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 154 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 0 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 1 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 2 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 1240 Z= 0.214 Angle : 0.493 8.446 1688 Z= 0.244 Chirality : 0.041 0.117 204 Planarity : 0.002 0.021 213 Dihedral : 5.027 48.350 197 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.36 % Allowed : 32.28 % Favored : 65.35 % 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: 0.94 (0.69), residues: 159 helix: 1.42 (0.66), residues: 55 sheet: -0.97 (0.98), residues: 26 loop : 0.83 (0.80), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 108 HIS 0.001 0.001 HIS A 54 PHE 0.001 0.000 PHE A 1 TYR 0.008 0.001 TYR A 50 ARG 0.002 0.000 ARG A 30 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 26 time to evaluate : 0.155 Fit side-chains REVERT: A 5 GLU cc_start: 0.6711 (OUTLIER) cc_final: 0.6215 (tp30) outliers start: 3 outliers final: 2 residues processed: 27 average time/residue: 0.6916 time to fit residues: 19.1714 Evaluate side-chains 29 residues out of total 128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 26 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 154 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 13 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 2 optimal weight: 0.0870 chunk 10 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 5 optimal weight: 0.4980 chunk 4 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.077015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.065710 restraints weight = 2231.846| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 2.32 r_work: 0.2745 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2637 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 1240 Z= 0.176 Angle : 0.477 8.316 1688 Z= 0.235 Chirality : 0.040 0.117 204 Planarity : 0.002 0.021 213 Dihedral : 4.930 48.203 197 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.36 % Allowed : 32.28 % Favored : 65.35 % 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: 0.96 (0.69), residues: 159 helix: 1.46 (0.66), residues: 55 sheet: -0.94 (0.98), residues: 26 loop : 0.82 (0.80), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 108 HIS 0.001 0.001 HIS A 54 PHE 0.001 0.000 PHE A 1 TYR 0.007 0.001 TYR A 50 ARG 0.001 0.000 ARG A 30 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1063.60 seconds wall clock time: 21 minutes 17.81 seconds (1277.81 seconds total)