Starting phenix.real_space_refine on Thu Jun 5 04:51:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p71_17514/06_2025/8p71_17514.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p71_17514/06_2025/8p71_17514.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8p71_17514/06_2025/8p71_17514.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p71_17514/06_2025/8p71_17514.map" model { file = "/net/cci-nas-00/data/ceres_data/8p71_17514/06_2025/8p71_17514.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p71_17514/06_2025/8p71_17514.cif" } resolution = 2.0 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= -0.000 sd= 0.001 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 31 5.16 5 C 3289 2.51 5 N 870 2.21 5 O 1027 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 5217 Number of models: 1 Model: "" Number of chains: 7 Chain: "H" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 512 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 5, 'TRANS': 59} Chain: "I" Number of atoms: 2281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2281 Unusual residues: {'ACE': 1} Classifications: {'peptide': 279, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 264} Chain breaks: 1 Chain: "J" Number of atoms: 2283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2283 Classifications: {'peptide': 286} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 267} Chain breaks: 2 Chain: "J" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'X4F': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "I" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "J" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 61 Classifications: {'water': 61} Link IDs: {None: 60} Time building chain proxies: 4.58, per 1000 atoms: 0.88 Number of scatterers: 5217 At special positions: 0 Unit cell: (84.7875, 94.05, 67.6875, 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 31 16.00 O 1027 8.00 N 870 7.00 C 3289 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.59 Conformation dependent library (CDL) restraints added in 574.9 milliseconds 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1196 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 3 sheets defined 63.0% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'H' and resid 262 through 264 No H-bonds generated for 'chain 'H' and resid 262 through 264' Processing helix chain 'H' and resid 265 through 270 Processing helix chain 'H' and resid 271 through 275 removed outlier: 3.587A pdb=" N VAL H 275 " --> pdb=" O LEU H 272 " (cutoff:3.500A) Processing helix chain 'H' and resid 279 through 285 Processing helix chain 'H' and resid 288 through 302 removed outlier: 3.850A pdb=" N ALA H 292 " --> pdb=" O THR H 288 " (cutoff:3.500A) Processing helix chain 'I' and resid 1 through 4 Processing helix chain 'I' and resid 5 through 11 Processing helix chain 'I' and resid 15 through 38 Processing helix chain 'I' and resid 49 through 70 Processing helix chain 'I' and resid 76 through 93 removed outlier: 3.853A pdb=" N ASN I 93 " --> pdb=" O ARG I 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 100 through 116 removed outlier: 3.554A pdb=" N LEU I 106 " --> pdb=" O ARG I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 121 through 127 Processing helix chain 'I' and resid 132 through 154 removed outlier: 4.626A pdb=" N LEU I 148 " --> pdb=" O LEU I 144 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LEU I 149 " --> pdb=" O GLU I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 163 through 178 Processing helix chain 'I' and resid 183 through 186 removed outlier: 3.772A pdb=" N ILE I 186 " --> pdb=" O ASN I 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 183 through 186' Processing helix chain 'I' and resid 187 through 201 removed outlier: 3.543A pdb=" N THR I 201 " --> pdb=" O ARG I 197 " (cutoff:3.500A) Processing helix chain 'I' and resid 202 through 206 Processing helix chain 'I' and resid 208 through 224 Processing helix chain 'I' and resid 228 through 234 removed outlier: 3.897A pdb=" N LEU I 232 " --> pdb=" O MET I 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 241 through 261 Processing helix chain 'I' and resid 266 through 284 Processing helix chain 'J' and resid 56 through 68 removed outlier: 3.766A pdb=" N GLU J 68 " --> pdb=" O LYS J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 98 through 104 Processing helix chain 'J' and resid 110 through 131 Processing helix chain 'J' and resid 139 through 141 No H-bonds generated for 'chain 'J' and resid 139 through 141' Processing helix chain 'J' and resid 155 through 159 removed outlier: 4.262A pdb=" N LEU J 158 " --> pdb=" O ASP J 155 " (cutoff:3.500A) Processing helix chain 'J' and resid 175 through 179 Processing helix chain 'J' and resid 180 through 185 Processing helix chain 'J' and resid 192 through 209 Processing helix chain 'J' and resid 217 through 230 Processing helix chain 'J' and resid 239 through 243 Processing helix chain 'J' and resid 256 through 261 Processing helix chain 'J' and resid 265 through 276 Processing helix chain 'J' and resid 285 through 292 Processing helix chain 'J' and resid 292 through 297 removed outlier: 3.738A pdb=" N SER J 296 " --> pdb=" O MET J 292 " (cutoff:3.500A) Processing helix chain 'J' and resid 303 through 307 Processing sheet with id=AA1, first strand: chain 'J' and resid 13 through 20 removed outlier: 6.616A pdb=" N LYS J 28 " --> pdb=" O LEU J 15 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N PHE J 17 " --> pdb=" O VAL J 26 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N VAL J 26 " --> pdb=" O PHE J 17 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP J 79 " --> pdb=" O VAL J 90 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ASP J 92 " --> pdb=" O LEU J 77 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N LEU J 77 " --> pdb=" O ASP J 92 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 96 through 97 Processing sheet with id=AA3, first strand: chain 'J' and resid 133 through 134 271 hydrogen bonds defined for protein. 765 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.23 Time building geometry restraints manager: 1.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1642 1.34 - 1.46: 1189 1.46 - 1.58: 2346 1.58 - 1.70: 1 1.70 - 1.82: 49 Bond restraints: 5227 Sorted by residual: bond pdb=" C08 X4F J 401 " pdb=" N09 X4F J 401 " ideal model delta sigma weight residual 1.342 1.491 -0.149 2.00e-02 2.50e+03 5.55e+01 bond pdb=" C02 X4F J 401 " pdb=" C04 X4F J 401 " ideal model delta sigma weight residual 1.502 1.596 -0.094 2.00e-02 2.50e+03 2.23e+01 bond pdb=" C18 X4F J 401 " pdb=" N19 X4F J 401 " ideal model delta sigma weight residual 1.365 1.454 -0.089 2.00e-02 2.50e+03 1.97e+01 bond pdb=" C10 X4F J 401 " pdb=" N09 X4F J 401 " ideal model delta sigma weight residual 1.451 1.510 -0.059 2.00e-02 2.50e+03 8.85e+00 bond pdb=" C27 X4F J 401 " pdb=" N26 X4F J 401 " ideal model delta sigma weight residual 1.344 1.395 -0.051 2.00e-02 2.50e+03 6.59e+00 ... (remaining 5222 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 6885 1.41 - 2.82: 135 2.82 - 4.23: 45 4.23 - 5.64: 8 5.64 - 7.04: 2 Bond angle restraints: 7075 Sorted by residual: angle pdb=" CB MET J 189 " pdb=" CG MET J 189 " pdb=" SD MET J 189 " ideal model delta sigma weight residual 112.70 119.74 -7.04 3.00e+00 1.11e-01 5.51e+00 angle pdb=" CA TYR I 91 " pdb=" CB TYR I 91 " pdb=" CG TYR I 91 " ideal model delta sigma weight residual 113.90 109.96 3.94 1.80e+00 3.09e-01 4.80e+00 angle pdb=" C04 X4F J 401 " pdb=" C05 X4F J 401 " pdb=" N06 X4F J 401 " ideal model delta sigma weight residual 113.81 107.42 6.39 3.00e+00 1.11e-01 4.54e+00 angle pdb=" CB GLU H 262 " pdb=" CG GLU H 262 " pdb=" CD GLU H 262 " ideal model delta sigma weight residual 112.60 116.04 -3.44 1.70e+00 3.46e-01 4.09e+00 angle pdb=" C17 X4F J 401 " pdb=" C08 X4F J 401 " pdb=" N09 X4F J 401 " ideal model delta sigma weight residual 126.29 120.82 5.47 3.00e+00 1.11e-01 3.32e+00 ... (remaining 7070 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.15: 2695 16.15 - 32.31: 325 32.31 - 48.46: 99 48.46 - 64.61: 35 64.61 - 80.76: 12 Dihedral angle restraints: 3166 sinusoidal: 1319 harmonic: 1847 Sorted by residual: dihedral pdb=" CA TYR I 91 " pdb=" C TYR I 91 " pdb=" N LEU I 92 " pdb=" CA LEU I 92 " ideal model delta harmonic sigma weight residual 180.00 162.72 17.28 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA THR I 176 " pdb=" C THR I 176 " pdb=" N ARG I 177 " pdb=" CA ARG I 177 " ideal model delta harmonic sigma weight residual -180.00 -162.79 -17.21 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA GLN H 281 " pdb=" CB GLN H 281 " pdb=" CG GLN H 281 " pdb=" CD GLN H 281 " ideal model delta sinusoidal sigma weight residual 60.00 119.99 -59.99 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 3163 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 448 0.026 - 0.052: 192 0.052 - 0.077: 83 0.077 - 0.103: 40 0.103 - 0.129: 14 Chirality restraints: 777 Sorted by residual: chirality pdb=" CA TYR I 91 " pdb=" N TYR I 91 " pdb=" C TYR I 91 " pdb=" CB TYR I 91 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.16e-01 chirality pdb=" CA ILE J 74 " pdb=" N ILE J 74 " pdb=" C ILE J 74 " pdb=" CB ILE J 74 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.97e-01 chirality pdb=" CA ILE J 255 " pdb=" N ILE J 255 " pdb=" C ILE J 255 " pdb=" CB ILE J 255 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.92e-01 ... (remaining 774 not shown) Planarity restraints: 903 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS J 139 " 0.020 5.00e-02 4.00e+02 2.96e-02 1.41e+00 pdb=" N PRO J 140 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO J 140 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO J 140 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL J 210 " -0.018 5.00e-02 4.00e+02 2.78e-02 1.24e+00 pdb=" N PRO J 211 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO J 211 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO J 211 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU I 49 " 0.017 5.00e-02 4.00e+02 2.59e-02 1.08e+00 pdb=" N PRO I 50 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO I 50 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO I 50 " 0.015 5.00e-02 4.00e+02 ... (remaining 900 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 870 2.76 - 3.29: 5174 3.29 - 3.83: 9865 3.83 - 4.36: 11471 4.36 - 4.90: 19039 Nonbonded interactions: 46419 Sorted by model distance: nonbonded pdb=" O HOH J 503 " pdb=" O HOH J 551 " model vdw 2.223 3.040 nonbonded pdb=" O TRP I 11 " pdb=" O HOH I 401 " model vdw 2.228 3.040 nonbonded pdb=" OD2 ASP J 92 " pdb=" O HOH J 501 " model vdw 2.233 3.040 nonbonded pdb=" O HOH J 536 " pdb=" O HOH J 554 " model vdw 2.257 3.040 nonbonded pdb=" O HOH J 502 " pdb=" O HOH J 552 " model vdw 2.258 3.040 ... (remaining 46414 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 16.620 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:18.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 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 0.149 5227 Z= 0.206 Angle : 0.549 7.044 7075 Z= 0.265 Chirality : 0.039 0.129 777 Planarity : 0.004 0.030 903 Dihedral : 16.922 80.763 1970 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 0.72 % Allowed : 20.04 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.72 (0.34), residues: 618 helix: 1.89 (0.28), residues: 346 sheet: -0.80 (1.11), residues: 20 loop : 0.37 (0.40), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP J 132 HIS 0.002 0.001 HIS J 258 PHE 0.014 0.002 PHE J 91 TYR 0.014 0.001 TYR I 2 ARG 0.003 0.000 ARG J 188 Details of bonding type rmsd hydrogen bonds : bond 0.12377 ( 271) hydrogen bonds : angle 5.79837 ( 765) covalent geometry : bond 0.00423 ( 5227) covalent geometry : angle 0.54936 ( 7075) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 90 time to evaluate : 0.578 Fit side-chains REVERT: I 232 LEU cc_start: 0.8173 (mm) cc_final: 0.7884 (mm) REVERT: J 252 PHE cc_start: 0.6732 (m-80) cc_final: 0.6433 (m-10) outliers start: 4 outliers final: 3 residues processed: 94 average time/residue: 1.5260 time to fit residues: 148.3843 Evaluate side-chains 91 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 88 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 44 ASP Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 158 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 0.0980 chunk 46 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 31 optimal weight: 0.0270 chunk 25 optimal weight: 0.5980 chunk 48 optimal weight: 7.9990 chunk 18 optimal weight: 0.4980 chunk 29 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 overall best weight: 0.3638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 18 GLN I 124 GLN J 297 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.180987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.158436 restraints weight = 4643.536| |-----------------------------------------------------------------------------| r_work (start): 0.3927 rms_B_bonded: 0.99 r_work: 0.3820 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3722 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.0662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 5227 Z= 0.103 Angle : 0.487 5.148 7075 Z= 0.249 Chirality : 0.039 0.125 777 Planarity : 0.004 0.034 903 Dihedral : 5.385 59.664 713 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 2.53 % Allowed : 18.05 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.34), residues: 618 helix: 2.06 (0.28), residues: 351 sheet: 0.42 (1.22), residues: 16 loop : 0.49 (0.41), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 132 HIS 0.004 0.001 HIS J 131 PHE 0.013 0.001 PHE I 110 TYR 0.015 0.001 TYR I 91 ARG 0.002 0.000 ARG H 295 Details of bonding type rmsd hydrogen bonds : bond 0.04287 ( 271) hydrogen bonds : angle 4.52865 ( 765) covalent geometry : bond 0.00212 ( 5227) covalent geometry : angle 0.48674 ( 7075) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.615 Fit side-chains REVERT: I 232 LEU cc_start: 0.8065 (mm) cc_final: 0.7765 (mm) REVERT: J 252 PHE cc_start: 0.6706 (m-80) cc_final: 0.6363 (m-10) outliers start: 14 outliers final: 8 residues processed: 103 average time/residue: 1.6697 time to fit residues: 178.3102 Evaluate side-chains 95 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain I residue 250 ASP Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 13 GLU Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain J residue 248 THR Chi-restraints excluded: chain J residue 292 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 15 optimal weight: 2.9990 chunk 61 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 5 optimal weight: 7.9990 chunk 49 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 24 optimal weight: 8.9990 chunk 27 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 18 GLN I 124 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.174799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.151902 restraints weight = 4658.353| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 0.98 r_work: 0.3740 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3642 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.1009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 5227 Z= 0.292 Angle : 0.713 7.914 7075 Z= 0.370 Chirality : 0.048 0.141 777 Planarity : 0.006 0.048 903 Dihedral : 6.109 57.890 709 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 3.07 % Allowed : 16.06 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.03 (0.33), residues: 618 helix: 1.32 (0.27), residues: 350 sheet: -0.86 (0.92), residues: 30 loop : 0.07 (0.40), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP J 132 HIS 0.006 0.002 HIS H 294 PHE 0.024 0.003 PHE J 91 TYR 0.025 0.003 TYR I 2 ARG 0.007 0.001 ARG I 23 Details of bonding type rmsd hydrogen bonds : bond 0.06163 ( 271) hydrogen bonds : angle 5.00317 ( 765) covalent geometry : bond 0.00646 ( 5227) covalent geometry : angle 0.71265 ( 7075) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.580 Fit side-chains REVERT: H 295 ARG cc_start: 0.7671 (OUTLIER) cc_final: 0.7417 (ttt-90) REVERT: I 63 ARG cc_start: 0.7604 (OUTLIER) cc_final: 0.7286 (mmm160) REVERT: I 85 MET cc_start: 0.7838 (tpp) cc_final: 0.7494 (tpp) REVERT: J 188 ARG cc_start: 0.6827 (OUTLIER) cc_final: 0.5676 (mmp80) outliers start: 17 outliers final: 10 residues processed: 106 average time/residue: 1.4781 time to fit residues: 162.1258 Evaluate side-chains 102 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 295 ARG Chi-restraints excluded: chain I residue 32 CYS Chi-restraints excluded: chain I residue 63 ARG Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain I residue 250 ASP Chi-restraints excluded: chain J residue 13 GLU Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain J residue 170 THR Chi-restraints excluded: chain J residue 188 ARG Chi-restraints excluded: chain J residue 248 THR Chi-restraints excluded: chain J residue 292 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 37 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 4 optimal weight: 7.9990 chunk 47 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 252 GLN I 18 GLN I 124 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.178011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.155247 restraints weight = 4756.010| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 1.00 r_work: 0.3780 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3681 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.0849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5227 Z= 0.137 Angle : 0.542 5.170 7075 Z= 0.279 Chirality : 0.041 0.170 777 Planarity : 0.004 0.045 903 Dihedral : 5.298 59.393 709 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 2.53 % Allowed : 16.61 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.66 (0.34), residues: 618 helix: 1.78 (0.28), residues: 351 sheet: 0.91 (1.28), residues: 15 loop : 0.24 (0.40), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP J 132 HIS 0.004 0.001 HIS J 131 PHE 0.014 0.002 PHE I 110 TYR 0.017 0.002 TYR I 2 ARG 0.003 0.000 ARG I 23 Details of bonding type rmsd hydrogen bonds : bond 0.04618 ( 271) hydrogen bonds : angle 4.54583 ( 765) covalent geometry : bond 0.00296 ( 5227) covalent geometry : angle 0.54189 ( 7075) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.589 Fit side-chains outliers start: 14 outliers final: 7 residues processed: 102 average time/residue: 1.5361 time to fit residues: 162.3297 Evaluate side-chains 100 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 93 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 32 CYS Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 250 ASP Chi-restraints excluded: chain J residue 13 GLU Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain J residue 248 THR Chi-restraints excluded: chain J residue 292 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 21 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 9 optimal weight: 6.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 18 GLN I 124 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.176253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.153276 restraints weight = 4631.869| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 0.99 r_work: 0.3756 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3658 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.0978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 5227 Z= 0.212 Angle : 0.627 5.645 7075 Z= 0.325 Chirality : 0.044 0.161 777 Planarity : 0.005 0.049 903 Dihedral : 5.614 58.567 709 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 3.25 % Allowed : 16.97 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.34 (0.34), residues: 618 helix: 1.56 (0.27), residues: 347 sheet: 1.01 (1.41), residues: 15 loop : 0.04 (0.40), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP I 11 HIS 0.005 0.001 HIS J 131 PHE 0.019 0.003 PHE J 91 TYR 0.022 0.002 TYR I 2 ARG 0.004 0.001 ARG I 23 Details of bonding type rmsd hydrogen bonds : bond 0.05394 ( 271) hydrogen bonds : angle 4.74678 ( 765) covalent geometry : bond 0.00467 ( 5227) covalent geometry : angle 0.62694 ( 7075) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 0.584 Fit side-chains REVERT: H 295 ARG cc_start: 0.7650 (OUTLIER) cc_final: 0.7401 (ttt-90) REVERT: I 63 ARG cc_start: 0.7609 (OUTLIER) cc_final: 0.7319 (mmm160) REVERT: I 85 MET cc_start: 0.7811 (tpp) cc_final: 0.7495 (tpp) outliers start: 18 outliers final: 11 residues processed: 105 average time/residue: 1.4425 time to fit residues: 156.9680 Evaluate side-chains 104 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 295 ARG Chi-restraints excluded: chain I residue 32 CYS Chi-restraints excluded: chain I residue 63 ARG Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 158 LEU Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain I residue 250 ASP Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 13 GLU Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 248 THR Chi-restraints excluded: chain J residue 292 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 9 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 18 optimal weight: 0.4980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 18 GLN I 124 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.178889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.156073 restraints weight = 4651.239| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 1.00 r_work: 0.3790 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3690 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.0877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 5227 Z= 0.124 Angle : 0.533 6.840 7075 Z= 0.272 Chirality : 0.041 0.156 777 Planarity : 0.004 0.053 903 Dihedral : 5.056 59.522 709 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 2.53 % Allowed : 18.05 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.71 (0.34), residues: 618 helix: 1.87 (0.28), residues: 351 sheet: 0.81 (1.32), residues: 15 loop : 0.20 (0.41), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP I 11 HIS 0.003 0.001 HIS I 100 PHE 0.015 0.002 PHE I 110 TYR 0.015 0.002 TYR I 2 ARG 0.003 0.000 ARG I 23 Details of bonding type rmsd hydrogen bonds : bond 0.04394 ( 271) hydrogen bonds : angle 4.44771 ( 765) covalent geometry : bond 0.00268 ( 5227) covalent geometry : angle 0.53293 ( 7075) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.641 Fit side-chains REVERT: J 227 GLU cc_start: 0.6978 (mt-10) cc_final: 0.6688 (mt-10) outliers start: 14 outliers final: 7 residues processed: 100 average time/residue: 1.4937 time to fit residues: 154.5740 Evaluate side-chains 94 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 32 CYS Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain I residue 250 ASP Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 13 GLU Chi-restraints excluded: chain J residue 248 THR Chi-restraints excluded: chain J residue 292 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 56 optimal weight: 0.0370 chunk 44 optimal weight: 0.9990 chunk 35 optimal weight: 9.9990 chunk 28 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 overall best weight: 1.0062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 252 GLN I 18 GLN I 124 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.178404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.155494 restraints weight = 4617.663| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 1.00 r_work: 0.3781 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3682 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.0912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5227 Z= 0.142 Angle : 0.552 7.474 7075 Z= 0.282 Chirality : 0.041 0.154 777 Planarity : 0.005 0.052 903 Dihedral : 5.014 59.814 708 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.54 % Rotamer: Outliers : 2.17 % Allowed : 19.31 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.76 (0.34), residues: 618 helix: 1.92 (0.28), residues: 348 sheet: 0.69 (1.28), residues: 15 loop : 0.22 (0.41), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP I 11 HIS 0.004 0.001 HIS J 131 PHE 0.015 0.002 PHE J 91 TYR 0.017 0.002 TYR I 2 ARG 0.003 0.000 ARG I 23 Details of bonding type rmsd hydrogen bonds : bond 0.04583 ( 271) hydrogen bonds : angle 4.46950 ( 765) covalent geometry : bond 0.00309 ( 5227) covalent geometry : angle 0.55158 ( 7075) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.583 Fit side-chains REVERT: H 295 ARG cc_start: 0.7631 (OUTLIER) cc_final: 0.7387 (ttt-90) REVERT: I 85 MET cc_start: 0.7764 (tpp) cc_final: 0.7532 (tpp) outliers start: 12 outliers final: 7 residues processed: 93 average time/residue: 1.6747 time to fit residues: 160.7655 Evaluate side-chains 96 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 295 ARG Chi-restraints excluded: chain I residue 32 CYS Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain I residue 250 ASP Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 13 GLU Chi-restraints excluded: chain J residue 248 THR Chi-restraints excluded: chain J residue 292 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 27 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 chunk 34 optimal weight: 5.9990 chunk 21 optimal weight: 0.0050 chunk 1 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 48 optimal weight: 6.9990 chunk 3 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 overall best weight: 0.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 124 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.178643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.156063 restraints weight = 4666.357| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 0.99 r_work: 0.3790 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3690 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.0904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5227 Z= 0.132 Angle : 0.544 8.046 7075 Z= 0.277 Chirality : 0.041 0.153 777 Planarity : 0.004 0.051 903 Dihedral : 4.956 59.881 708 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.54 % Rotamer: Outliers : 1.99 % Allowed : 19.68 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.34), residues: 618 helix: 1.99 (0.28), residues: 348 sheet: 0.68 (1.24), residues: 15 loop : 0.25 (0.41), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP I 11 HIS 0.003 0.001 HIS J 131 PHE 0.014 0.002 PHE I 110 TYR 0.016 0.002 TYR I 2 ARG 0.003 0.000 ARG I 23 Details of bonding type rmsd hydrogen bonds : bond 0.04423 ( 271) hydrogen bonds : angle 4.41308 ( 765) covalent geometry : bond 0.00288 ( 5227) covalent geometry : angle 0.54418 ( 7075) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.582 Fit side-chains REVERT: H 295 ARG cc_start: 0.7625 (OUTLIER) cc_final: 0.7391 (ttt-90) REVERT: I 85 MET cc_start: 0.7778 (tpp) cc_final: 0.7516 (tpp) REVERT: J 227 GLU cc_start: 0.7005 (mt-10) cc_final: 0.6699 (mt-10) outliers start: 11 outliers final: 7 residues processed: 98 average time/residue: 1.5911 time to fit residues: 161.1815 Evaluate side-chains 96 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 295 ARG Chi-restraints excluded: chain I residue 32 CYS Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain I residue 250 ASP Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 13 GLU Chi-restraints excluded: chain J residue 248 THR Chi-restraints excluded: chain J residue 292 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 44 optimal weight: 1.9990 chunk 48 optimal weight: 7.9990 chunk 8 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 50 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 31 optimal weight: 0.0970 chunk 27 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 252 GLN I 18 GLN I 124 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.180156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.157396 restraints weight = 4665.637| |-----------------------------------------------------------------------------| r_work (start): 0.3914 rms_B_bonded: 1.00 r_work: 0.3805 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3706 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.0962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5227 Z= 0.116 Angle : 0.533 9.214 7075 Z= 0.269 Chirality : 0.040 0.150 777 Planarity : 0.004 0.051 903 Dihedral : 4.855 59.806 708 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 1.62 % Allowed : 19.86 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.95 (0.34), residues: 618 helix: 2.10 (0.28), residues: 348 sheet: 0.23 (1.21), residues: 16 loop : 0.30 (0.41), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP I 11 HIS 0.003 0.001 HIS J 258 PHE 0.015 0.002 PHE I 110 TYR 0.015 0.002 TYR J 27 ARG 0.002 0.000 ARG I 23 Details of bonding type rmsd hydrogen bonds : bond 0.04157 ( 271) hydrogen bonds : angle 4.31440 ( 765) covalent geometry : bond 0.00253 ( 5227) covalent geometry : angle 0.53342 ( 7075) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 time to evaluate : 0.636 Fit side-chains REVERT: I 85 MET cc_start: 0.7790 (tpp) cc_final: 0.7552 (tpp) REVERT: J 107 LEU cc_start: 0.6516 (OUTLIER) cc_final: 0.6238 (pp) REVERT: J 227 GLU cc_start: 0.6981 (mt-10) cc_final: 0.6654 (mt-10) outliers start: 9 outliers final: 8 residues processed: 93 average time/residue: 1.5765 time to fit residues: 151.7448 Evaluate side-chains 94 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 32 CYS Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain I residue 250 ASP Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 13 GLU Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain J residue 248 THR Chi-restraints excluded: chain J residue 292 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 4 optimal weight: 7.9990 chunk 35 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 13 optimal weight: 9.9990 chunk 34 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 18 optimal weight: 0.0570 chunk 53 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 overall best weight: 1.3702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 124 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.177723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.154841 restraints weight = 4667.176| |-----------------------------------------------------------------------------| r_work (start): 0.3884 rms_B_bonded: 1.00 r_work: 0.3774 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3675 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.0947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5227 Z= 0.168 Angle : 0.591 8.954 7075 Z= 0.301 Chirality : 0.042 0.152 777 Planarity : 0.005 0.051 903 Dihedral : 5.059 58.913 708 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.13 % Favored : 98.71 % Rotamer: Outliers : 2.17 % Allowed : 19.86 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.71 (0.34), residues: 618 helix: 1.88 (0.28), residues: 348 sheet: 0.76 (1.25), residues: 15 loop : 0.21 (0.41), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP J 177 HIS 0.004 0.001 HIS J 131 PHE 0.017 0.002 PHE J 91 TYR 0.019 0.002 TYR I 2 ARG 0.004 0.001 ARG I 23 Details of bonding type rmsd hydrogen bonds : bond 0.04829 ( 271) hydrogen bonds : angle 4.51867 ( 765) covalent geometry : bond 0.00372 ( 5227) covalent geometry : angle 0.59137 ( 7075) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.651 Fit side-chains REVERT: I 85 MET cc_start: 0.7776 (tpp) cc_final: 0.7526 (tpp) REVERT: J 107 LEU cc_start: 0.6523 (OUTLIER) cc_final: 0.6270 (pp) outliers start: 12 outliers final: 9 residues processed: 94 average time/residue: 1.4925 time to fit residues: 145.4613 Evaluate side-chains 98 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 32 CYS Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain I residue 250 ASP Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 13 GLU Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain J residue 248 THR Chi-restraints excluded: chain J residue 292 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 21 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 chunk 51 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 252 GLN I 18 GLN I 124 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.178448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.155681 restraints weight = 4649.646| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 0.99 r_work: 0.3785 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3686 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.0943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5227 Z= 0.146 Angle : 0.572 8.576 7075 Z= 0.291 Chirality : 0.042 0.150 777 Planarity : 0.005 0.052 903 Dihedral : 5.008 59.602 708 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.54 % Rotamer: Outliers : 2.35 % Allowed : 19.49 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.77 (0.34), residues: 618 helix: 1.94 (0.28), residues: 348 sheet: 0.72 (1.23), residues: 15 loop : 0.22 (0.41), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP I 11 HIS 0.004 0.001 HIS J 131 PHE 0.015 0.002 PHE J 91 TYR 0.017 0.002 TYR I 2 ARG 0.003 0.000 ARG H 268 Details of bonding type rmsd hydrogen bonds : bond 0.04579 ( 271) hydrogen bonds : angle 4.46237 ( 765) covalent geometry : bond 0.00321 ( 5227) covalent geometry : angle 0.57172 ( 7075) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6258.27 seconds wall clock time: 108 minutes 7.98 seconds (6487.98 seconds total)