Starting phenix.real_space_refine on Wed Mar 5 15:29:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kom_62478/03_2025/9kom_62478.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kom_62478/03_2025/9kom_62478.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kom_62478/03_2025/9kom_62478.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kom_62478/03_2025/9kom_62478.map" model { file = "/net/cci-nas-00/data/ceres_data/9kom_62478/03_2025/9kom_62478.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kom_62478/03_2025/9kom_62478.cif" } resolution = 3.2 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= 0.052 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 10 5.16 5 C 1485 2.51 5 N 377 2.21 5 O 396 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 2268 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2268 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 13, 'TRANS': 277} Chain breaks: 4 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 50 Time building chain proxies: 2.35, per 1000 atoms: 1.04 Number of scatterers: 2268 At special positions: 0 Unit cell: (60.48, 50.4, 119.28, 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 10 16.00 O 396 8.00 N 377 7.00 C 1485 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 261 " distance=2.03 Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS A 242 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.55 Conformation dependent library (CDL) restraints added in 274.7 milliseconds 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 568 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 1 sheets defined 69.8% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 32 through 61 Proline residue: A 46 - end of helix removed outlier: 4.291A pdb=" N GLN A 56 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU A 57 " --> pdb=" O ALA A 53 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N SER A 59 " --> pdb=" O ALA A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 88 Processing helix chain 'A' and resid 104 through 109 removed outlier: 4.443A pdb=" N LYS A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 132 removed outlier: 3.545A pdb=" N ALA A 118 " --> pdb=" O LEU A 114 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A 119 " --> pdb=" O LEU A 115 " (cutoff:3.500A) Proline residue: A 124 - end of helix Processing helix chain 'A' and resid 132 through 159 removed outlier: 3.825A pdb=" N ARG A 156 " --> pdb=" O ASN A 152 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU A 157 " --> pdb=" O ARG A 153 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN A 159 " --> pdb=" O ILE A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 201 removed outlier: 3.991A pdb=" N LEU A 196 " --> pdb=" O LEU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 231 removed outlier: 3.809A pdb=" N ASN A 213 " --> pdb=" O TYR A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 235 removed outlier: 3.592A pdb=" N PHE A 235 " --> pdb=" O LEU A 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 232 through 235' Processing helix chain 'A' and resid 265 through 294 removed outlier: 3.967A pdb=" N VAL A 284 " --> pdb=" O TYR A 280 " (cutoff:3.500A) Proline residue: A 285 - end of helix removed outlier: 4.574A pdb=" N LEU A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 317 removed outlier: 3.634A pdb=" N LYS A 317 " --> pdb=" O LEU A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 336 Processing helix chain 'A' and resid 368 through 374 removed outlier: 4.295A pdb=" N GLY A 374 " --> pdb=" O THR A 370 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 66 137 hydrogen bonds defined for protein. 408 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: 0.53 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: 1.23 - 1.34: 698 1.34 - 1.46: 559 1.46 - 1.58: 1048 1.58 - 1.70: 0 1.70 - 1.81: 13 Bond restraints: 2318 Sorted by residual: bond pdb=" CB GLU A 193 " pdb=" CG GLU A 193 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.67e+00 bond pdb=" CB GLU A 252 " pdb=" CG GLU A 252 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.20e+00 bond pdb=" CB TYR A 151 " pdb=" CG TYR A 151 " ideal model delta sigma weight residual 1.512 1.535 -0.023 2.20e-02 2.07e+03 1.05e+00 bond pdb=" CB ASP A 148 " pdb=" CG ASP A 148 " ideal model delta sigma weight residual 1.516 1.541 -0.025 2.50e-02 1.60e+03 9.68e-01 bond pdb=" C TRP A 105 " pdb=" N PRO A 106 " ideal model delta sigma weight residual 1.335 1.346 -0.012 1.28e-02 6.10e+03 8.41e-01 ... (remaining 2313 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 3063 1.82 - 3.65: 58 3.65 - 5.47: 14 5.47 - 7.30: 14 7.30 - 9.12: 2 Bond angle restraints: 3151 Sorted by residual: angle pdb=" CA GLU A 193 " pdb=" CB GLU A 193 " pdb=" CG GLU A 193 " ideal model delta sigma weight residual 114.10 121.32 -7.22 2.00e+00 2.50e-01 1.30e+01 angle pdb=" CA TYR A 151 " pdb=" CB TYR A 151 " pdb=" CG TYR A 151 " ideal model delta sigma weight residual 113.90 120.40 -6.50 1.80e+00 3.09e-01 1.30e+01 angle pdb=" CB MET A 121 " pdb=" CG MET A 121 " pdb=" SD MET A 121 " ideal model delta sigma weight residual 112.70 121.82 -9.12 3.00e+00 1.11e-01 9.25e+00 angle pdb=" CA GLU A 252 " pdb=" CB GLU A 252 " pdb=" CG GLU A 252 " ideal model delta sigma weight residual 114.10 120.06 -5.96 2.00e+00 2.50e-01 8.88e+00 angle pdb=" CB GLU A 252 " pdb=" CG GLU A 252 " pdb=" CD GLU A 252 " ideal model delta sigma weight residual 112.60 117.60 -5.00 1.70e+00 3.46e-01 8.65e+00 ... (remaining 3146 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.00: 1135 16.00 - 32.01: 185 32.01 - 48.01: 60 48.01 - 64.01: 10 64.01 - 80.02: 3 Dihedral angle restraints: 1393 sinusoidal: 528 harmonic: 865 Sorted by residual: dihedral pdb=" CA GLU A 252 " pdb=" C GLU A 252 " pdb=" N THR A 253 " pdb=" CA THR A 253 " ideal model delta harmonic sigma weight residual 180.00 -164.60 -15.40 0 5.00e+00 4.00e-02 9.49e+00 dihedral pdb=" N ASN A 152 " pdb=" CA ASN A 152 " pdb=" CB ASN A 152 " pdb=" CG ASN A 152 " ideal model delta sinusoidal sigma weight residual -60.00 -116.98 56.98 3 1.50e+01 4.44e-03 9.42e+00 dihedral pdb=" CA HIS A 203 " pdb=" C HIS A 203 " pdb=" N SER A 204 " pdb=" CA SER A 204 " ideal model delta harmonic sigma weight residual -180.00 -164.71 -15.29 0 5.00e+00 4.00e-02 9.35e+00 ... (remaining 1390 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 233 0.030 - 0.060: 89 0.060 - 0.090: 40 0.090 - 0.120: 15 0.120 - 0.150: 4 Chirality restraints: 381 Sorted by residual: chirality pdb=" CA SER A 45 " pdb=" N SER A 45 " pdb=" C SER A 45 " pdb=" CB SER A 45 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.63e-01 chirality pdb=" CA TRP A 105 " pdb=" N TRP A 105 " pdb=" C TRP A 105 " pdb=" CB TRP A 105 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.94e-01 chirality pdb=" CA ILE A 64 " pdb=" N ILE A 64 " pdb=" C ILE A 64 " pdb=" CB ILE A 64 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.34e-01 ... (remaining 378 not shown) Planarity restraints: 383 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU A 193 " 0.010 2.00e-02 2.50e+03 2.11e-02 4.46e+00 pdb=" CD GLU A 193 " -0.037 2.00e-02 2.50e+03 pdb=" OE1 GLU A 193 " 0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU A 193 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 252 " 0.008 2.00e-02 2.50e+03 1.63e-02 2.67e+00 pdb=" CD GLU A 252 " -0.028 2.00e-02 2.50e+03 pdb=" OE1 GLU A 252 " 0.010 2.00e-02 2.50e+03 pdb=" OE2 GLU A 252 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP A 105 " -0.026 5.00e-02 4.00e+02 3.94e-02 2.48e+00 pdb=" N PRO A 106 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 106 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 106 " -0.022 5.00e-02 4.00e+02 ... (remaining 380 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 509 2.78 - 3.31: 2115 3.31 - 3.84: 3654 3.84 - 4.37: 3531 4.37 - 4.90: 6478 Nonbonded interactions: 16287 Sorted by model distance: nonbonded pdb=" OH TYR A 224 " pdb=" OG1 THR A 281 " model vdw 2.245 3.040 nonbonded pdb=" O PRO A 322 " pdb=" ND2 ASN A 327 " model vdw 2.308 3.120 nonbonded pdb=" N GLU A 238 " pdb=" OE1 GLU A 238 " model vdw 2.313 3.120 nonbonded pdb=" OD1 ASP A 35 " pdb=" ND2 ASN A 290 " model vdw 2.330 3.120 nonbonded pdb=" O ARG A 156 " pdb=" NE2 GLN A 159 " model vdw 2.334 3.120 ... (remaining 16282 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: 1.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 10.980 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6096 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 0.043 2318 Z= 0.251 Angle : 0.786 9.122 3151 Z= 0.400 Chirality : 0.042 0.150 381 Planarity : 0.004 0.039 383 Dihedral : 17.934 80.018 819 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 0.81 % Allowed : 41.13 % Favored : 58.06 % 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: 0.32 (0.52), residues: 281 helix: 1.05 (0.39), residues: 189 sheet: -1.11 (1.37), residues: 18 loop : -1.55 (0.72), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 297 HIS 0.001 0.000 HIS A 90 PHE 0.018 0.002 PHE A 189 TYR 0.009 0.001 TYR A 280 ARG 0.000 0.000 ARG A 316 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 38 time to evaluate : 0.247 Fit side-chains REVERT: A 29 ARG cc_start: 0.6910 (ttm-80) cc_final: 0.6607 (ttp-110) REVERT: A 129 GLN cc_start: 0.6987 (tp40) cc_final: 0.6477 (tt0) REVERT: A 194 ARG cc_start: 0.6344 (mtm-85) cc_final: 0.5518 (tmt170) REVERT: A 201 ARG cc_start: 0.7109 (mmm-85) cc_final: 0.6291 (ttm110) REVERT: A 237 GLN cc_start: 0.7236 (tp40) cc_final: 0.6987 (tp40) REVERT: A 239 GLU cc_start: 0.8092 (pt0) cc_final: 0.7826 (pt0) REVERT: A 257 ASN cc_start: 0.7784 (t0) cc_final: 0.7263 (t0) REVERT: A 262 ARG cc_start: 0.6598 (ttt90) cc_final: 0.6202 (ttm-80) REVERT: A 331 LEU cc_start: 0.4607 (mt) cc_final: 0.4329 (mp) REVERT: A 334 ARG cc_start: 0.6149 (tmm-80) cc_final: 0.5511 (tmm160) outliers start: 2 outliers final: 0 residues processed: 40 average time/residue: 0.2361 time to fit residues: 10.5795 Evaluate side-chains 28 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 24 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.167155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.121845 restraints weight = 2369.370| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.70 r_work: 0.3159 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2318 Z= 0.206 Angle : 0.607 7.303 3151 Z= 0.298 Chirality : 0.038 0.127 381 Planarity : 0.004 0.035 383 Dihedral : 3.762 14.981 311 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 4.03 % Allowed : 38.31 % Favored : 57.66 % 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: 0.68 (0.52), residues: 281 helix: 1.33 (0.38), residues: 194 sheet: -1.17 (1.32), residues: 18 loop : -1.57 (0.73), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 297 HIS 0.002 0.001 HIS A 91 PHE 0.008 0.001 PHE A 269 TYR 0.012 0.001 TYR A 280 ARG 0.002 0.000 ARG A 75 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 27 time to evaluate : 0.253 Fit side-chains REVERT: A 29 ARG cc_start: 0.7510 (ttm-80) cc_final: 0.7190 (ttp-110) REVERT: A 200 GLN cc_start: 0.6748 (tm-30) cc_final: 0.6463 (tt0) REVERT: A 201 ARG cc_start: 0.7526 (mmm-85) cc_final: 0.6814 (ttm110) REVERT: A 262 ARG cc_start: 0.8492 (ttt90) cc_final: 0.8110 (ttm-80) REVERT: A 334 ARG cc_start: 0.7558 (tmm-80) cc_final: 0.6942 (tmm160) outliers start: 10 outliers final: 6 residues processed: 37 average time/residue: 0.1986 time to fit residues: 8.4850 Evaluate side-chains 29 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 23 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 72 PHE Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 277 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 23 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 chunk 3 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.166200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.119567 restraints weight = 2367.231| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.74 r_work: 0.3128 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2318 Z= 0.192 Angle : 0.560 6.895 3151 Z= 0.271 Chirality : 0.038 0.123 381 Planarity : 0.005 0.057 383 Dihedral : 3.548 14.329 311 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 6.05 % Allowed : 35.89 % Favored : 58.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.52), residues: 281 helix: 1.63 (0.39), residues: 192 sheet: -1.11 (1.31), residues: 18 loop : -1.71 (0.70), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 105 HIS 0.002 0.001 HIS A 91 PHE 0.009 0.001 PHE A 269 TYR 0.011 0.001 TYR A 280 ARG 0.001 0.000 ARG A 153 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 27 time to evaluate : 0.258 Fit side-chains REVERT: A 29 ARG cc_start: 0.7515 (ttm-80) cc_final: 0.7044 (ttm170) REVERT: A 108 LYS cc_start: 0.8593 (ttpp) cc_final: 0.8119 (tttm) REVERT: A 200 GLN cc_start: 0.6968 (tm-30) cc_final: 0.6598 (tt0) REVERT: A 201 ARG cc_start: 0.7576 (mmm-85) cc_final: 0.6927 (ttm110) REVERT: A 233 ASP cc_start: 0.8025 (m-30) cc_final: 0.7773 (m-30) REVERT: A 262 ARG cc_start: 0.8472 (ttt90) cc_final: 0.8083 (ttm-80) REVERT: A 334 ARG cc_start: 0.7404 (tmm-80) cc_final: 0.6852 (tmm160) outliers start: 15 outliers final: 10 residues processed: 40 average time/residue: 0.2145 time to fit residues: 9.7824 Evaluate side-chains 34 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 24 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 72 PHE Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 318 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 19 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 12 optimal weight: 9.9990 chunk 4 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.160338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.115108 restraints weight = 2384.692| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 1.62 r_work: 0.3121 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2318 Z= 0.199 Angle : 0.542 6.669 3151 Z= 0.264 Chirality : 0.038 0.124 381 Planarity : 0.004 0.046 383 Dihedral : 3.437 14.354 311 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 5.65 % Allowed : 37.10 % Favored : 57.26 % 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: 1.08 (0.52), residues: 281 helix: 1.72 (0.39), residues: 192 sheet: -0.91 (1.33), residues: 18 loop : -1.65 (0.70), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 105 HIS 0.002 0.001 HIS A 91 PHE 0.010 0.001 PHE A 269 TYR 0.011 0.001 TYR A 280 ARG 0.001 0.000 ARG A 153 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 25 time to evaluate : 0.249 Fit side-chains REVERT: A 29 ARG cc_start: 0.7561 (ttm-80) cc_final: 0.7118 (ttm170) REVERT: A 201 ARG cc_start: 0.7663 (mmm-85) cc_final: 0.7088 (ttm110) REVERT: A 233 ASP cc_start: 0.7911 (m-30) cc_final: 0.7676 (m-30) REVERT: A 334 ARG cc_start: 0.7462 (tmm-80) cc_final: 0.6891 (tmm160) outliers start: 14 outliers final: 12 residues processed: 38 average time/residue: 0.1967 time to fit residues: 8.6157 Evaluate side-chains 35 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 23 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 72 PHE Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 318 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 27 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 28 optimal weight: 0.0270 chunk 16 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 10 optimal weight: 0.1980 chunk 23 optimal weight: 0.5980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.161478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.115947 restraints weight = 2400.702| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.69 r_work: 0.3162 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 2318 Z= 0.162 Angle : 0.512 6.624 3151 Z= 0.249 Chirality : 0.037 0.120 381 Planarity : 0.004 0.038 383 Dihedral : 3.270 14.263 311 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 4.44 % Allowed : 37.90 % Favored : 57.66 % 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: 1.31 (0.52), residues: 281 helix: 1.90 (0.38), residues: 192 sheet: -0.90 (1.31), residues: 18 loop : -1.58 (0.70), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 105 HIS 0.001 0.000 HIS A 91 PHE 0.008 0.001 PHE A 269 TYR 0.009 0.001 TYR A 280 ARG 0.001 0.000 ARG A 75 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 25 time to evaluate : 0.266 Fit side-chains REVERT: A 201 ARG cc_start: 0.7641 (mmm-85) cc_final: 0.7058 (ttm110) REVERT: A 233 ASP cc_start: 0.7846 (m-30) cc_final: 0.7593 (m-30) REVERT: A 334 ARG cc_start: 0.7511 (tmm-80) cc_final: 0.6926 (tmm160) outliers start: 11 outliers final: 9 residues processed: 35 average time/residue: 0.2128 time to fit residues: 8.4893 Evaluate side-chains 33 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 24 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 72 PHE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 318 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 7 optimal weight: 0.7980 chunk 4 optimal weight: 0.0770 chunk 22 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.158940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.114227 restraints weight = 2365.778| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.65 r_work: 0.3131 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2318 Z= 0.183 Angle : 0.522 6.647 3151 Z= 0.255 Chirality : 0.037 0.122 381 Planarity : 0.004 0.035 383 Dihedral : 3.302 14.326 311 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 6.45 % Allowed : 35.48 % Favored : 58.06 % 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: 1.32 (0.52), residues: 281 helix: 1.91 (0.38), residues: 192 sheet: -0.82 (1.30), residues: 18 loop : -1.60 (0.70), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 105 HIS 0.002 0.001 HIS A 91 PHE 0.010 0.001 PHE A 269 TYR 0.010 0.001 TYR A 280 ARG 0.001 0.000 ARG A 75 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 23 time to evaluate : 0.200 Fit side-chains REVERT: A 201 ARG cc_start: 0.7743 (mmm-85) cc_final: 0.7177 (ttm110) REVERT: A 233 ASP cc_start: 0.7953 (m-30) cc_final: 0.7690 (m-30) REVERT: A 334 ARG cc_start: 0.7506 (tmm-80) cc_final: 0.6951 (tmm160) outliers start: 16 outliers final: 13 residues processed: 38 average time/residue: 0.1973 time to fit residues: 8.6327 Evaluate side-chains 37 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 24 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 72 PHE Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 318 MET Chi-restraints excluded: chain A residue 328 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 20 optimal weight: 1.9990 chunk 22 optimal weight: 0.0770 chunk 7 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 3 optimal weight: 0.4980 chunk 15 optimal weight: 0.6980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.162259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.116431 restraints weight = 2422.256| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.68 r_work: 0.3163 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 2318 Z= 0.158 Angle : 0.521 7.901 3151 Z= 0.248 Chirality : 0.036 0.119 381 Planarity : 0.004 0.033 383 Dihedral : 3.175 14.002 311 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 4.84 % Allowed : 36.29 % Favored : 58.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.52), residues: 281 helix: 2.02 (0.38), residues: 194 sheet: -0.81 (1.28), residues: 18 loop : -1.43 (0.71), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 105 HIS 0.001 0.000 HIS A 91 PHE 0.009 0.001 PHE A 269 TYR 0.009 0.001 TYR A 280 ARG 0.001 0.000 ARG A 293 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 24 time to evaluate : 0.269 Fit side-chains REVERT: A 201 ARG cc_start: 0.7696 (mmm-85) cc_final: 0.7130 (ttm110) REVERT: A 233 ASP cc_start: 0.7936 (m-30) cc_final: 0.7667 (m-30) REVERT: A 334 ARG cc_start: 0.7504 (tmm-80) cc_final: 0.6940 (tmm160) outliers start: 12 outliers final: 11 residues processed: 35 average time/residue: 0.2152 time to fit residues: 8.7047 Evaluate side-chains 35 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 24 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 72 PHE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 318 MET Chi-restraints excluded: chain A residue 328 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 2 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 6 optimal weight: 0.0970 chunk 15 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 7 optimal weight: 0.0980 chunk 3 optimal weight: 0.0010 chunk 13 optimal weight: 4.9990 chunk 22 optimal weight: 0.5980 overall best weight: 0.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.172398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.128204 restraints weight = 2448.195| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.67 r_work: 0.3198 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 2318 Z= 0.145 Angle : 0.506 7.151 3151 Z= 0.241 Chirality : 0.036 0.118 381 Planarity : 0.004 0.034 383 Dihedral : 3.072 13.495 311 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 5.65 % Allowed : 34.27 % Favored : 60.08 % 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: 1.72 (0.52), residues: 281 helix: 2.22 (0.38), residues: 192 sheet: -0.76 (1.27), residues: 18 loop : -1.45 (0.70), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 105 HIS 0.001 0.000 HIS A 254 PHE 0.008 0.001 PHE A 269 TYR 0.008 0.001 TYR A 280 ARG 0.001 0.000 ARG A 75 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 24 time to evaluate : 0.252 Fit side-chains REVERT: A 201 ARG cc_start: 0.7724 (mmm-85) cc_final: 0.7157 (ttm110) REVERT: A 233 ASP cc_start: 0.7735 (m-30) cc_final: 0.7470 (m-30) REVERT: A 334 ARG cc_start: 0.7539 (tmm-80) cc_final: 0.6984 (tmm160) outliers start: 14 outliers final: 14 residues processed: 37 average time/residue: 0.1963 time to fit residues: 8.4359 Evaluate side-chains 38 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 24 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 72 PHE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 242 CYS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 318 MET Chi-restraints excluded: chain A residue 328 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 8 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.159416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.113398 restraints weight = 2412.343| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.68 r_work: 0.3121 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2318 Z= 0.206 Angle : 0.545 7.234 3151 Z= 0.262 Chirality : 0.037 0.122 381 Planarity : 0.004 0.033 383 Dihedral : 3.271 14.378 311 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 5.24 % Allowed : 34.27 % Favored : 60.48 % 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: 1.60 (0.51), residues: 281 helix: 2.12 (0.38), residues: 192 sheet: -0.57 (1.29), residues: 18 loop : -1.52 (0.69), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 105 HIS 0.002 0.001 HIS A 91 PHE 0.011 0.001 PHE A 269 TYR 0.012 0.001 TYR A 280 ARG 0.001 0.000 ARG A 75 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 23 time to evaluate : 0.249 Fit side-chains REVERT: A 201 ARG cc_start: 0.7718 (mmm-85) cc_final: 0.7168 (ttm110) REVERT: A 233 ASP cc_start: 0.8023 (m-30) cc_final: 0.7767 (m-30) REVERT: A 334 ARG cc_start: 0.7430 (tmm-80) cc_final: 0.6911 (tmm160) outliers start: 13 outliers final: 13 residues processed: 35 average time/residue: 0.1848 time to fit residues: 7.5656 Evaluate side-chains 34 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 21 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 72 PHE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 242 CYS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 318 MET Chi-restraints excluded: chain A residue 328 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 21 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 19 optimal weight: 0.0170 chunk 1 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 24 optimal weight: 10.0000 chunk 6 optimal weight: 0.8980 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.167189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.122382 restraints weight = 2379.565| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.63 r_work: 0.3142 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2318 Z= 0.177 Angle : 0.527 6.931 3151 Z= 0.253 Chirality : 0.037 0.120 381 Planarity : 0.004 0.033 383 Dihedral : 3.232 14.595 311 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 5.65 % Allowed : 34.68 % Favored : 59.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.51), residues: 281 helix: 2.19 (0.38), residues: 192 sheet: -0.65 (1.27), residues: 18 loop : -1.53 (0.68), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 105 HIS 0.002 0.001 HIS A 91 PHE 0.009 0.001 PHE A 269 TYR 0.010 0.001 TYR A 280 ARG 0.001 0.000 ARG A 75 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 23 time to evaluate : 0.232 Fit side-chains REVERT: A 201 ARG cc_start: 0.7676 (mmm-85) cc_final: 0.7140 (ttm110) REVERT: A 233 ASP cc_start: 0.7972 (m-30) cc_final: 0.7706 (m-30) REVERT: A 334 ARG cc_start: 0.7514 (tmm-80) cc_final: 0.6979 (tmm160) outliers start: 14 outliers final: 13 residues processed: 36 average time/residue: 0.1724 time to fit residues: 7.3389 Evaluate side-chains 36 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 23 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 72 PHE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 242 CYS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 318 MET Chi-restraints excluded: chain A residue 328 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 4 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 11 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 19 optimal weight: 0.0470 chunk 10 optimal weight: 0.9980 chunk 28 optimal weight: 0.0980 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.161532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.117397 restraints weight = 2378.738| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.65 r_work: 0.3179 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 2318 Z= 0.153 Angle : 0.515 6.896 3151 Z= 0.246 Chirality : 0.037 0.118 381 Planarity : 0.004 0.034 383 Dihedral : 3.148 13.995 311 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 4.84 % Allowed : 35.48 % Favored : 59.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.52), residues: 281 helix: 2.23 (0.38), residues: 192 sheet: -0.74 (1.26), residues: 18 loop : -1.49 (0.69), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 105 HIS 0.001 0.000 HIS A 254 PHE 0.008 0.001 PHE A 269 TYR 0.008 0.001 TYR A 280 ARG 0.001 0.000 ARG A 293 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1750.09 seconds wall clock time: 30 minutes 40.47 seconds (1840.47 seconds total)