Starting phenix.real_space_refine on Tue Feb 11 02:50:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sdz_40355/02_2025/8sdz_40355.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sdz_40355/02_2025/8sdz_40355.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sdz_40355/02_2025/8sdz_40355.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sdz_40355/02_2025/8sdz_40355.map" model { file = "/net/cci-nas-00/data/ceres_data/8sdz_40355/02_2025/8sdz_40355.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sdz_40355/02_2025/8sdz_40355.cif" } resolution = 2.86 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= 0.002 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 2533 2.51 5 N 654 2.21 5 O 695 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 3913 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3872 Classifications: {'peptide': 500} Link IDs: {'PTRANS': 26, 'TRANS': 473} Chain breaks: 3 Chain: "A" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 41 Unusual residues: {'RTO': 1} Classifications: {'undetermined': 1, 'water': 22} Link IDs: {None: 22} Time building chain proxies: 2.81, per 1000 atoms: 0.72 Number of scatterers: 3913 At special positions: 0 Unit cell: (78.85, 71.38, 98.77, 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 695 8.00 N 654 7.00 C 2533 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 105 " distance=2.03 Simple disulfide: pdb=" SG CYS A 78 " - pdb=" SG CYS A 128 " distance=2.02 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: 0.97 Conformation dependent library (CDL) restraints added in 431.6 milliseconds 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 928 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 2 sheets defined 80.4% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 2 through 10 Processing helix chain 'A' and resid 14 through 26 Processing helix chain 'A' and resid 27 through 36 removed outlier: 3.963A pdb=" N ALA A 32 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N SER A 33 " --> pdb=" O LEU A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 42 Processing helix chain 'A' and resid 62 through 66 Processing helix chain 'A' and resid 119 through 125 Processing helix chain 'A' and resid 127 through 130 Processing helix chain 'A' and resid 131 through 160 removed outlier: 4.115A pdb=" N GLN A 135 " --> pdb=" O ARG A 131 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP A 157 " --> pdb=" O GLY A 153 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG A 158 " --> pdb=" O TYR A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 181 Processing helix chain 'A' and resid 184 through 213 removed outlier: 3.569A pdb=" N SER A 198 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER A 201 " --> pdb=" O MET A 197 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TRP A 213 " --> pdb=" O LEU A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 217 removed outlier: 6.057A pdb=" N HIS A 217 " --> pdb=" O MET A 214 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 214 through 217' Processing helix chain 'A' and resid 218 through 244 removed outlier: 3.585A pdb=" N VAL A 222 " --> pdb=" O THR A 218 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN A 234 " --> pdb=" O TYR A 230 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 254 Processing helix chain 'A' and resid 256 through 265 removed outlier: 3.711A pdb=" N ILE A 260 " --> pdb=" O VAL A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 271 through 278 Processing helix chain 'A' and resid 280 through 296 Processing helix chain 'A' and resid 297 through 304 Processing helix chain 'A' and resid 305 through 314 Processing helix chain 'A' and resid 327 through 332 Processing helix chain 'A' and resid 332 through 355 removed outlier: 3.580A pdb=" N HIS A 337 " --> pdb=" O PRO A 333 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU A 338 " --> pdb=" O THR A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 377 Processing helix chain 'A' and resid 377 through 392 Processing helix chain 'A' and resid 393 through 415 Processing helix chain 'A' and resid 419 through 449 Processing helix chain 'A' and resid 453 through 477 Proline residue: A 473 - end of helix Processing helix chain 'A' and resid 478 through 481 Processing helix chain 'A' and resid 484 through 502 Proline residue: A 494 - end of helix removed outlier: 3.880A pdb=" N ALA A 502 " --> pdb=" O SER A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 524 removed outlier: 3.834A pdb=" N LEU A 519 " --> pdb=" O THR A 515 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 49 Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 81 272 hydrogen bonds defined for protein. 801 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: 1.19 Time building geometry restraints manager: 1.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1217 1.35 - 1.46: 974 1.46 - 1.58: 1743 1.58 - 1.70: 0 1.70 - 1.82: 49 Bond restraints: 3983 Sorted by residual: bond pdb=" N04 RTO A 601 " pdb=" S08 RTO A 601 " ideal model delta sigma weight residual 1.625 1.712 -0.087 2.00e-02 2.50e+03 1.88e+01 bond pdb=" C11 RTO A 601 " pdb=" S08 RTO A 601 " ideal model delta sigma weight residual 1.776 1.820 -0.044 2.00e-02 2.50e+03 4.78e+00 bond pdb=" CB PRO A 505 " pdb=" CG PRO A 505 " ideal model delta sigma weight residual 1.492 1.568 -0.076 5.00e-02 4.00e+02 2.32e+00 bond pdb=" CB MET A 23 " pdb=" CG MET A 23 " ideal model delta sigma weight residual 1.520 1.544 -0.024 3.00e-02 1.11e+03 6.28e-01 bond pdb=" O09 RTO A 601 " pdb=" S08 RTO A 601 " ideal model delta sigma weight residual 1.446 1.462 -0.016 2.00e-02 2.50e+03 6.14e-01 ... (remaining 3978 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.62: 5394 3.62 - 7.23: 23 7.23 - 10.85: 1 10.85 - 14.46: 0 14.46 - 18.08: 1 Bond angle restraints: 5419 Sorted by residual: angle pdb=" O09 RTO A 601 " pdb=" S08 RTO A 601 " pdb=" O10 RTO A 601 " ideal model delta sigma weight residual 119.19 101.11 18.08 3.00e+00 1.11e-01 3.63e+01 angle pdb=" CB MET A 23 " pdb=" CG MET A 23 " pdb=" SD MET A 23 " ideal model delta sigma weight residual 112.70 122.34 -9.64 3.00e+00 1.11e-01 1.03e+01 angle pdb=" CA MET A 23 " pdb=" CB MET A 23 " pdb=" CG MET A 23 " ideal model delta sigma weight residual 114.10 119.50 -5.40 2.00e+00 2.50e-01 7.29e+00 angle pdb=" CA TYR A 264 " pdb=" CB TYR A 264 " pdb=" CG TYR A 264 " ideal model delta sigma weight residual 113.90 118.00 -4.10 1.80e+00 3.09e-01 5.20e+00 angle pdb=" N VAL A 256 " pdb=" CA VAL A 256 " pdb=" C VAL A 256 " ideal model delta sigma weight residual 108.88 113.75 -4.87 2.16e+00 2.14e-01 5.09e+00 ... (remaining 5414 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.88: 2037 16.88 - 33.76: 237 33.76 - 50.64: 70 50.64 - 67.52: 18 67.52 - 84.40: 7 Dihedral angle restraints: 2369 sinusoidal: 926 harmonic: 1443 Sorted by residual: dihedral pdb=" CA CYS A 49 " pdb=" CB CYS A 49 " pdb=" SG CYS A 49 " pdb=" SG CYS A 105 " ideal model delta sinusoidal sigma weight residual -73.00 2.02 -75.02 1 2.00e+01 2.50e-03 1.78e+01 dihedral pdb=" CB CYS A 49 " pdb=" SG CYS A 49 " pdb=" SG CYS A 105 " pdb=" CB CYS A 105 " ideal model delta sinusoidal sigma weight residual -86.00 -113.39 27.39 1 1.00e+01 1.00e-02 1.08e+01 dihedral pdb=" SG CYS A 49 " pdb=" CB CYS A 105 " pdb=" SG CYS A 105 " pdb=" CA CYS A 105 " ideal model delta sinusoidal sigma weight residual 79.00 24.03 54.97 1 2.00e+01 2.50e-03 1.02e+01 ... (remaining 2366 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 487 0.039 - 0.077: 116 0.077 - 0.116: 22 0.116 - 0.154: 4 0.154 - 0.193: 2 Chirality restraints: 631 Sorted by residual: chirality pdb=" CG LEU A 6 " pdb=" CB LEU A 6 " pdb=" CD1 LEU A 6 " pdb=" CD2 LEU A 6 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.28e-01 chirality pdb=" CG LEU A 232 " pdb=" CB LEU A 232 " pdb=" CD1 LEU A 232 " pdb=" CD2 LEU A 232 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.46e-01 chirality pdb=" CA ILE A 44 " pdb=" N ILE A 44 " pdb=" C ILE A 44 " pdb=" CB ILE A 44 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.72e-01 ... (remaining 628 not shown) Planarity restraints: 673 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 213 " 0.014 2.00e-02 2.50e+03 1.38e-02 4.79e+00 pdb=" CG TRP A 213 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP A 213 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP A 213 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 213 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP A 213 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 213 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 213 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 213 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 213 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 26 " -0.019 5.00e-02 4.00e+02 2.85e-02 1.30e+00 pdb=" N PRO A 27 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO A 27 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 27 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 256 " -0.017 5.00e-02 4.00e+02 2.52e-02 1.02e+00 pdb=" N PRO A 257 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO A 257 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 257 " -0.014 5.00e-02 4.00e+02 ... (remaining 670 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 67 2.69 - 3.24: 3898 3.24 - 3.79: 6341 3.79 - 4.35: 8704 4.35 - 4.90: 14135 Nonbonded interactions: 33145 Sorted by model distance: nonbonded pdb=" O VAL A 475 " pdb=" OG1 THR A 478 " model vdw 2.135 3.040 nonbonded pdb=" OG SER A 33 " pdb=" O HOH A 701 " model vdw 2.191 3.040 nonbonded pdb=" OD1 ASN A 168 " pdb=" OG SER A 201 " model vdw 2.211 3.040 nonbonded pdb=" O LEU A 29 " pdb=" O HOH A 701 " model vdw 2.216 3.040 nonbonded pdb=" O GLY A 233 " pdb=" O HOH A 701 " model vdw 2.234 3.040 ... (remaining 33140 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: 0.010 Normalize map: mean=0, sd=1: 0.190 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.130 Find NCS groups from input model: 0.040 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:12.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 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 : 0.003 0.087 3983 Z= 0.164 Angle : 0.588 18.076 5419 Z= 0.261 Chirality : 0.036 0.193 631 Planarity : 0.003 0.028 673 Dihedral : 16.554 84.396 1435 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 1.43 % Allowed : 20.24 % Favored : 78.33 % 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: 0.91 (0.37), residues: 492 helix: 0.73 (0.26), residues: 374 sheet: 0.04 (1.43), residues: 10 loop : 0.67 (0.63), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 213 HIS 0.001 0.000 HIS A 48 PHE 0.007 0.001 PHE A 191 TYR 0.013 0.001 TYR A 264 ARG 0.002 0.000 ARG A 336 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.449 Fit side-chains REVERT: A 280 ARG cc_start: 0.5134 (mmm160) cc_final: 0.4856 (tpp-160) outliers start: 6 outliers final: 5 residues processed: 65 average time/residue: 1.1617 time to fit residues: 78.2532 Evaluate side-chains 60 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 337 HIS Chi-restraints excluded: chain A residue 515 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 39 optimal weight: 0.0030 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 0.0170 chunk 29 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 overall best weight: 0.5628 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 ASN A 246 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.174720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.133359 restraints weight = 4338.209| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.09 r_work: 0.3374 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3983 Z= 0.159 Angle : 0.545 7.304 5419 Z= 0.270 Chirality : 0.038 0.169 631 Planarity : 0.004 0.028 673 Dihedral : 6.974 62.599 571 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 3.57 % Allowed : 18.81 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.39), residues: 492 helix: 1.53 (0.27), residues: 368 sheet: 0.67 (1.36), residues: 10 loop : 1.05 (0.65), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 213 HIS 0.002 0.001 HIS A 48 PHE 0.017 0.001 PHE A 351 TYR 0.019 0.001 TYR A 264 ARG 0.002 0.000 ARG A 131 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 0.405 Fit side-chains revert: symmetry clash REVERT: A 219 ARG cc_start: 0.4582 (ttt-90) cc_final: 0.4243 (mtt90) REVERT: A 327 MET cc_start: 0.5936 (OUTLIER) cc_final: 0.5606 (mmm) outliers start: 15 outliers final: 5 residues processed: 69 average time/residue: 1.0481 time to fit residues: 75.2096 Evaluate side-chains 60 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 327 MET Chi-restraints excluded: chain A residue 337 HIS Chi-restraints excluded: chain A residue 500 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 38 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 28 optimal weight: 7.9990 chunk 39 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 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 295 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.174620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.133369 restraints weight = 4293.796| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.07 r_work: 0.3367 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3983 Z= 0.160 Angle : 0.490 6.184 5419 Z= 0.246 Chirality : 0.037 0.127 631 Planarity : 0.003 0.026 673 Dihedral : 6.617 64.850 566 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 3.57 % Allowed : 19.05 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.39), residues: 492 helix: 1.63 (0.27), residues: 369 sheet: 0.61 (1.30), residues: 10 loop : 1.10 (0.66), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 213 HIS 0.002 0.000 HIS A 48 PHE 0.016 0.001 PHE A 351 TYR 0.018 0.001 TYR A 264 ARG 0.003 0.000 ARG A 134 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.438 Fit side-chains revert: symmetry clash REVERT: A 4 ASN cc_start: 0.7435 (m-40) cc_final: 0.6727 (t0) REVERT: A 344 MET cc_start: 0.7054 (OUTLIER) cc_final: 0.6094 (mpp) REVERT: A 447 GLU cc_start: 0.8312 (mt-10) cc_final: 0.8105 (mt-10) outliers start: 15 outliers final: 6 residues processed: 66 average time/residue: 0.9974 time to fit residues: 68.7550 Evaluate side-chains 61 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 337 HIS Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 500 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 30 optimal weight: 4.9990 chunk 6 optimal weight: 0.4980 chunk 14 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 1 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 2 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.173588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.132102 restraints weight = 4332.910| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.08 r_work: 0.3361 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3983 Z= 0.166 Angle : 0.494 7.747 5419 Z= 0.245 Chirality : 0.037 0.124 631 Planarity : 0.003 0.025 673 Dihedral : 6.597 62.074 566 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 3.57 % Allowed : 17.86 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.39), residues: 492 helix: 1.64 (0.27), residues: 368 sheet: 0.22 (1.33), residues: 10 loop : 0.96 (0.65), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 213 HIS 0.002 0.000 HIS A 48 PHE 0.015 0.001 PHE A 351 TYR 0.022 0.001 TYR A 264 ARG 0.003 0.000 ARG A 134 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 0.401 Fit side-chains revert: symmetry clash REVERT: A 4 ASN cc_start: 0.7410 (m-40) cc_final: 0.6747 (t0) REVERT: A 386 PHE cc_start: 0.7029 (m-10) cc_final: 0.6273 (t80) REVERT: A 431 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.7663 (tmtm) outliers start: 15 outliers final: 8 residues processed: 70 average time/residue: 0.9195 time to fit residues: 67.3798 Evaluate side-chains 65 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 337 HIS Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 500 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 32 optimal weight: 0.9990 chunk 6 optimal weight: 8.9990 chunk 4 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.3975 r_free = 0.3975 target = 0.173972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.132912 restraints weight = 4439.915| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.10 r_work: 0.3335 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3983 Z= 0.161 Angle : 0.483 5.750 5419 Z= 0.240 Chirality : 0.037 0.135 631 Planarity : 0.003 0.024 673 Dihedral : 6.599 61.941 566 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 4.29 % Allowed : 17.86 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.39), residues: 492 helix: 1.72 (0.27), residues: 369 sheet: 0.16 (1.38), residues: 10 loop : 0.89 (0.65), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 213 HIS 0.002 0.000 HIS A 48 PHE 0.015 0.001 PHE A 351 TYR 0.020 0.001 TYR A 264 ARG 0.003 0.000 ARG A 134 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 57 time to evaluate : 0.421 Fit side-chains revert: symmetry clash REVERT: A 4 ASN cc_start: 0.7526 (m-40) cc_final: 0.6772 (t0) REVERT: A 386 PHE cc_start: 0.7039 (m-10) cc_final: 0.6264 (t80) REVERT: A 431 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.7709 (tmtm) outliers start: 18 outliers final: 9 residues processed: 71 average time/residue: 0.8726 time to fit residues: 64.9983 Evaluate side-chains 67 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 337 HIS Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 500 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 7 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 43 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 8 optimal weight: 8.9990 chunk 33 optimal weight: 0.2980 chunk 11 optimal weight: 0.6980 chunk 42 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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 = 0.3932 r_free = 0.3932 target = 0.168948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.127792 restraints weight = 4388.984| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.04 r_work: 0.3285 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3983 Z= 0.255 Angle : 0.544 8.705 5419 Z= 0.271 Chirality : 0.039 0.128 631 Planarity : 0.004 0.026 673 Dihedral : 6.908 66.623 566 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 4.29 % Allowed : 17.86 % Favored : 77.86 % 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: 1.87 (0.38), residues: 492 helix: 1.51 (0.27), residues: 368 sheet: 0.14 (1.59), residues: 10 loop : 0.73 (0.65), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 213 HIS 0.003 0.001 HIS A 337 PHE 0.015 0.002 PHE A 191 TYR 0.013 0.001 TYR A 264 ARG 0.003 0.000 ARG A 134 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 56 time to evaluate : 0.439 Fit side-chains revert: symmetry clash REVERT: A 4 ASN cc_start: 0.7582 (m-40) cc_final: 0.7147 (t0) REVERT: A 6 LEU cc_start: 0.6433 (OUTLIER) cc_final: 0.6191 (mm) REVERT: A 386 PHE cc_start: 0.7233 (m-10) cc_final: 0.6388 (t80) REVERT: A 431 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.7712 (tmtm) outliers start: 18 outliers final: 9 residues processed: 71 average time/residue: 0.9055 time to fit residues: 67.2785 Evaluate side-chains 67 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 337 HIS Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 500 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 12 optimal weight: 0.8980 chunk 20 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 26 optimal weight: 9.9990 chunk 38 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- 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 = 0.3934 r_free = 0.3934 target = 0.169547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.128510 restraints weight = 4403.445| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.07 r_work: 0.3316 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3983 Z= 0.229 Angle : 0.530 7.042 5419 Z= 0.266 Chirality : 0.038 0.126 631 Planarity : 0.004 0.026 673 Dihedral : 6.910 65.385 566 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 4.52 % Allowed : 17.38 % Favored : 78.10 % 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: 1.87 (0.39), residues: 492 helix: 1.54 (0.27), residues: 368 sheet: 0.02 (1.70), residues: 10 loop : 0.63 (0.65), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 213 HIS 0.003 0.001 HIS A 48 PHE 0.014 0.001 PHE A 351 TYR 0.018 0.001 TYR A 264 ARG 0.002 0.000 ARG A 134 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 58 time to evaluate : 0.405 Fit side-chains revert: symmetry clash REVERT: A 4 ASN cc_start: 0.7595 (m-40) cc_final: 0.7205 (t0) REVERT: A 207 MET cc_start: 0.6102 (OUTLIER) cc_final: 0.5496 (tpt) REVERT: A 386 PHE cc_start: 0.7166 (m-10) cc_final: 0.6326 (t80) REVERT: A 431 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.7727 (tmtm) outliers start: 19 outliers final: 11 residues processed: 73 average time/residue: 0.8440 time to fit residues: 64.6678 Evaluate side-chains 70 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 337 HIS Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 500 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 7 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 49 optimal weight: 10.0000 chunk 17 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 15 optimal weight: 6.9990 chunk 26 optimal weight: 10.0000 chunk 10 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 40 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 = 0.3966 r_free = 0.3966 target = 0.172899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.132232 restraints weight = 4361.518| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.08 r_work: 0.3322 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3983 Z= 0.165 Angle : 0.514 6.558 5419 Z= 0.252 Chirality : 0.037 0.125 631 Planarity : 0.004 0.026 673 Dihedral : 6.783 61.930 566 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 3.81 % Allowed : 17.38 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.39), residues: 492 helix: 1.70 (0.27), residues: 369 sheet: 0.09 (1.71), residues: 10 loop : 0.64 (0.65), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 213 HIS 0.002 0.001 HIS A 48 PHE 0.014 0.001 PHE A 351 TYR 0.021 0.001 TYR A 264 ARG 0.003 0.000 ARG A 134 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 57 time to evaluate : 0.388 Fit side-chains revert: symmetry clash REVERT: A 207 MET cc_start: 0.6054 (OUTLIER) cc_final: 0.5479 (tpt) REVERT: A 273 ARG cc_start: 0.6558 (ttm170) cc_final: 0.6302 (mtm180) REVERT: A 386 PHE cc_start: 0.7124 (m-10) cc_final: 0.6317 (t80) REVERT: A 431 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.7736 (tmtm) outliers start: 16 outliers final: 11 residues processed: 70 average time/residue: 0.9160 time to fit residues: 67.0570 Evaluate side-chains 69 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 337 HIS Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 500 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 6 optimal weight: 5.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.3962 r_free = 0.3962 target = 0.172615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.132079 restraints weight = 4368.169| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.08 r_work: 0.3316 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3983 Z= 0.180 Angle : 0.523 7.541 5419 Z= 0.257 Chirality : 0.038 0.127 631 Planarity : 0.004 0.026 673 Dihedral : 6.802 62.402 566 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 3.57 % Allowed : 18.10 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.39), residues: 492 helix: 1.70 (0.27), residues: 369 sheet: -0.15 (1.61), residues: 10 loop : 0.70 (0.65), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 213 HIS 0.002 0.000 HIS A 48 PHE 0.014 0.001 PHE A 351 TYR 0.020 0.001 TYR A 264 ARG 0.003 0.000 ARG A 134 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 57 time to evaluate : 0.419 Fit side-chains revert: symmetry clash REVERT: A 207 MET cc_start: 0.6040 (OUTLIER) cc_final: 0.5470 (tpt) REVERT: A 273 ARG cc_start: 0.6559 (ttm170) cc_final: 0.6244 (mtm180) REVERT: A 328 GLU cc_start: 0.6583 (tp30) cc_final: 0.6362 (tp30) REVERT: A 386 PHE cc_start: 0.7141 (m-10) cc_final: 0.6289 (t80) REVERT: A 431 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.7747 (tmtm) outliers start: 15 outliers final: 11 residues processed: 69 average time/residue: 0.9605 time to fit residues: 69.0969 Evaluate side-chains 71 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 337 HIS Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 500 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 41 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 29 optimal weight: 9.9990 chunk 19 optimal weight: 0.0050 chunk 44 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 48 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 overall best weight: 1.1398 ------------------------------------------------------------------------------- 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 = 0.3959 r_free = 0.3959 target = 0.172068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.131758 restraints weight = 4348.459| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.06 r_work: 0.3317 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 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 : 0.003 0.034 3983 Z= 0.185 Angle : 0.545 9.512 5419 Z= 0.264 Chirality : 0.038 0.127 631 Planarity : 0.004 0.026 673 Dihedral : 6.834 62.436 566 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 3.57 % Allowed : 18.81 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.39), residues: 492 helix: 1.68 (0.27), residues: 369 sheet: -0.12 (1.62), residues: 10 loop : 0.75 (0.65), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.003 TRP A 213 HIS 0.002 0.000 HIS A 48 PHE 0.014 0.001 PHE A 351 TYR 0.020 0.001 TYR A 264 ARG 0.002 0.000 ARG A 134 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 0.418 Fit side-chains revert: symmetry clash REVERT: A 207 MET cc_start: 0.6044 (OUTLIER) cc_final: 0.5485 (tpt) REVERT: A 232 LEU cc_start: 0.8294 (mp) cc_final: 0.8076 (OUTLIER) REVERT: A 328 GLU cc_start: 0.6597 (tp30) cc_final: 0.5639 (pt0) REVERT: A 386 PHE cc_start: 0.7144 (m-10) cc_final: 0.6295 (t80) REVERT: A 431 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.7757 (tmtm) outliers start: 15 outliers final: 12 residues processed: 72 average time/residue: 0.9604 time to fit residues: 72.4043 Evaluate side-chains 73 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 337 HIS Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 500 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 44 optimal weight: 0.5980 chunk 1 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 28 optimal weight: 9.9990 chunk 38 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3967 r_free = 0.3967 target = 0.173036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.133044 restraints weight = 4310.578| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.05 r_work: 0.3320 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3983 Z= 0.184 Angle : 0.538 9.143 5419 Z= 0.262 Chirality : 0.038 0.126 631 Planarity : 0.004 0.025 673 Dihedral : 6.798 62.242 566 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 3.33 % Allowed : 19.05 % Favored : 77.62 % 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: 1.97 (0.39), residues: 492 helix: 1.59 (0.27), residues: 375 sheet: -0.08 (1.62), residues: 10 loop : 0.70 (0.66), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.003 TRP A 213 HIS 0.002 0.000 HIS A 48 PHE 0.014 0.001 PHE A 351 TYR 0.020 0.001 TYR A 264 ARG 0.003 0.000 ARG A 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3000.61 seconds wall clock time: 53 minutes 36.26 seconds (3216.26 seconds total)