Starting phenix.real_space_refine on Sat Apr 26 23:32:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sdz_40355/04_2025/8sdz_40355.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sdz_40355/04_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_40355/04_2025/8sdz_40355.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sdz_40355/04_2025/8sdz_40355.map" model { file = "/net/cci-nas-00/data/ceres_data/8sdz_40355/04_2025/8sdz_40355.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sdz_40355/04_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-5669/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: 2.92, per 1000 atoms: 0.75 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: 1.02 Conformation dependent library (CDL) restraints added in 480.1 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: 0.41 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: 1.15 Time building geometry restraints manager: 1.18 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: 0.000 Normalize map: mean=0, sd=1: 0.320 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.310 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.980 ------------------------------------------------------------------------------- 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 3985 Z= 0.130 Angle : 0.588 18.076 5423 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 Details of bonding type rmsd hydrogen bonds : bond 0.23340 ( 272) hydrogen bonds : angle 7.31566 ( 801) SS BOND : bond 0.00518 ( 2) SS BOND : angle 0.80018 ( 4) covalent geometry : bond 0.00299 ( 3983) covalent geometry : angle 0.58831 ( 5419) *********************** 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 : 0.383 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: 1.1128 time to fit residues: 74.9932 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 : 0.431 ------------------------------------------------------------------------------- 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 = 37)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.133361 restraints weight = 4338.209| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.09 r_work: 0.3375 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 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 3985 Z= 0.131 Angle : 0.545 7.304 5423 Z= 0.270 Chirality : 0.038 0.169 631 Planarity : 0.004 0.028 673 Dihedral : 6.974 62.600 571 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 Details of bonding type rmsd hydrogen bonds : bond 0.05373 ( 272) hydrogen bonds : angle 4.74673 ( 801) SS BOND : bond 0.00603 ( 2) SS BOND : angle 0.57174 ( 4) covalent geometry : bond 0.00255 ( 3983) covalent geometry : angle 0.54507 ( 5419) *********************** 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 : 0.417 Fit side-chains revert: symmetry clash REVERT: A 219 ARG cc_start: 0.4579 (ttt-90) cc_final: 0.4240 (mtt90) REVERT: A 327 MET cc_start: 0.5928 (OUTLIER) cc_final: 0.5600 (mmm) outliers start: 15 outliers final: 5 residues processed: 69 average time/residue: 1.0009 time to fit residues: 72.0010 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 : 0.665 ------------------------------------------------------------------------------- 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: 0.9990 chunk 17 optimal weight: 0.7980 chunk 49 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 28 optimal weight: 7.9990 chunk 39 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 = 0.3988 r_free = 0.3988 target = 0.174750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.133546 restraints weight = 4301.110| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.08 r_work: 0.3347 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 3985 Z= 0.121 Angle : 0.490 6.157 5423 Z= 0.247 Chirality : 0.037 0.125 631 Planarity : 0.003 0.026 673 Dihedral : 6.616 64.678 566 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 3.81 % Allowed : 18.81 % 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: 1.62 (0.27), residues: 369 sheet: 0.65 (1.31), residues: 10 loop : 1.10 (0.66), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 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 Details of bonding type rmsd hydrogen bonds : bond 0.04622 ( 272) hydrogen bonds : angle 4.37423 ( 801) SS BOND : bond 0.00595 ( 2) SS BOND : angle 0.68142 ( 4) covalent geometry : bond 0.00249 ( 3983) covalent geometry : angle 0.48965 ( 5419) *********************** 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 72 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 56 time to evaluate : 0.382 Fit side-chains revert: symmetry clash REVERT: A 4 ASN cc_start: 0.7430 (m-40) cc_final: 0.6739 (t0) REVERT: A 344 MET cc_start: 0.7059 (OUTLIER) cc_final: 0.6091 (mpp) REVERT: A 447 GLU cc_start: 0.8304 (mt-10) cc_final: 0.8093 (mt-10) outliers start: 16 outliers final: 6 residues processed: 67 average time/residue: 0.9441 time to fit residues: 66.0931 Evaluate side-chains 64 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.419 ------------------------------------------------------------------------------- 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: 5.9990 chunk 6 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 1 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 chunk 27 optimal weight: 7.9990 chunk 18 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 = 0.3954 r_free = 0.3954 target = 0.171361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.129649 restraints weight = 4346.605| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.09 r_work: 0.3331 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3985 Z= 0.146 Angle : 0.519 7.787 5423 Z= 0.259 Chirality : 0.038 0.124 631 Planarity : 0.004 0.026 673 Dihedral : 6.738 64.552 566 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 4.29 % Allowed : 17.38 % 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: 1.94 (0.38), residues: 492 helix: 1.52 (0.27), residues: 368 sheet: 0.31 (1.35), residues: 10 loop : 0.88 (0.65), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 213 HIS 0.003 0.001 HIS A 48 PHE 0.014 0.002 PHE A 351 TYR 0.018 0.001 TYR A 264 ARG 0.003 0.000 ARG A 134 Details of bonding type rmsd hydrogen bonds : bond 0.04636 ( 272) hydrogen bonds : angle 4.31616 ( 801) SS BOND : bond 0.00881 ( 2) SS BOND : angle 0.87435 ( 4) covalent geometry : bond 0.00329 ( 3983) covalent geometry : angle 0.51829 ( 5419) *********************** 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 76 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 58 time to evaluate : 0.431 Fit side-chains revert: symmetry clash REVERT: A 4 ASN cc_start: 0.7502 (m-40) cc_final: 0.6759 (t0) REVERT: A 344 MET cc_start: 0.7102 (OUTLIER) cc_final: 0.6086 (mpp) REVERT: A 386 PHE cc_start: 0.7114 (m-10) cc_final: 0.6263 (t80) REVERT: A 417 LYS cc_start: 0.8255 (mmtm) cc_final: 0.8039 (mppt) REVERT: A 431 LYS cc_start: 0.8689 (OUTLIER) cc_final: 0.7707 (tmtm) outliers start: 18 outliers final: 9 residues processed: 71 average time/residue: 0.9347 time to fit residues: 69.3286 Evaluate side-chains 66 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.387 ------------------------------------------------------------------------------- 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 344 MET 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: 3.9990 chunk 33 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 15 optimal weight: 8.9990 chunk 47 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 32 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- 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 = 0.3943 r_free = 0.3943 target = 0.170320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.128994 restraints weight = 4471.074| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.10 r_work: 0.3293 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3985 Z= 0.149 Angle : 0.514 6.396 5423 Z= 0.258 Chirality : 0.038 0.127 631 Planarity : 0.004 0.026 673 Dihedral : 6.834 64.917 566 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 4.05 % Allowed : 17.86 % 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 (0.38), residues: 492 helix: 1.50 (0.27), residues: 368 sheet: 0.21 (1.39), residues: 10 loop : 0.76 (0.64), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 213 HIS 0.003 0.001 HIS A 48 PHE 0.014 0.001 PHE A 351 TYR 0.017 0.001 TYR A 264 ARG 0.003 0.000 ARG A 134 Details of bonding type rmsd hydrogen bonds : bond 0.04558 ( 272) hydrogen bonds : angle 4.26159 ( 801) SS BOND : bond 0.00894 ( 2) SS BOND : angle 0.92287 ( 4) covalent geometry : bond 0.00338 ( 3983) covalent geometry : angle 0.51349 ( 5419) *********************** 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 72 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 55 time to evaluate : 0.428 Fit side-chains revert: symmetry clash REVERT: A 4 ASN cc_start: 0.7626 (m-40) cc_final: 0.7179 (t0) REVERT: A 344 MET cc_start: 0.7106 (OUTLIER) cc_final: 0.6121 (mpp) REVERT: A 386 PHE cc_start: 0.7160 (m-10) cc_final: 0.6317 (t80) REVERT: A 417 LYS cc_start: 0.8260 (mmtm) cc_final: 0.8020 (mppt) REVERT: A 431 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.7669 (tmtm) outliers start: 17 outliers final: 9 residues processed: 68 average time/residue: 0.9353 time to fit residues: 66.4421 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 : 0.398 ------------------------------------------------------------------------------- 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 344 MET 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: 2.9990 chunk 19 optimal weight: 8.9990 chunk 43 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 11 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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 = 0.3899 r_free = 0.3899 target = 0.164040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.122805 restraints weight = 4402.424| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.06 r_work: 0.3254 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 3985 Z= 0.218 Angle : 0.595 8.338 5423 Z= 0.299 Chirality : 0.041 0.135 631 Planarity : 0.004 0.029 673 Dihedral : 7.283 70.586 566 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 5.48 % Allowed : 16.43 % 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: 1.53 (0.38), residues: 492 helix: 1.27 (0.27), residues: 368 sheet: 0.09 (1.49), residues: 10 loop : 0.59 (0.65), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP A 213 HIS 0.004 0.001 HIS A 48 PHE 0.014 0.002 PHE A 191 TYR 0.011 0.001 TYR A 354 ARG 0.002 0.000 ARG A 134 Details of bonding type rmsd hydrogen bonds : bond 0.05188 ( 272) hydrogen bonds : angle 4.48951 ( 801) SS BOND : bond 0.01344 ( 2) SS BOND : angle 1.29230 ( 4) covalent geometry : bond 0.00525 ( 3983) covalent geometry : angle 0.59390 ( 5419) *********************** 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 78 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 55 time to evaluate : 0.455 Fit side-chains revert: symmetry clash REVERT: A 4 ASN cc_start: 0.7629 (m-40) cc_final: 0.7243 (t0) REVERT: A 207 MET cc_start: 0.6170 (OUTLIER) cc_final: 0.5511 (tpt) REVERT: A 328 GLU cc_start: 0.6604 (tp30) cc_final: 0.6402 (tp30) REVERT: A 344 MET cc_start: 0.7201 (OUTLIER) cc_final: 0.6060 (mpp) REVERT: A 431 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.7751 (tmtm) outliers start: 23 outliers final: 9 residues processed: 71 average time/residue: 0.8831 time to fit residues: 65.7070 Evaluate side-chains 66 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 264 TYR Chi-restraints excluded: chain A residue 337 HIS Chi-restraints excluded: chain A residue 344 MET 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: 0.7980 chunk 20 optimal weight: 10.0000 chunk 36 optimal weight: 4.9990 chunk 7 optimal weight: 0.3980 chunk 49 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 38 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- 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 = 0.3955 r_free = 0.3955 target = 0.171599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.130572 restraints weight = 4360.355| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.07 r_work: 0.3339 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3985 Z= 0.120 Angle : 0.513 6.922 5423 Z= 0.255 Chirality : 0.037 0.125 631 Planarity : 0.004 0.027 673 Dihedral : 6.883 62.127 566 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 5.24 % Allowed : 17.14 % 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: 1.89 (0.39), residues: 492 helix: 1.53 (0.27), residues: 368 sheet: 0.03 (1.50), residues: 10 loop : 0.70 (0.64), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 213 HIS 0.002 0.001 HIS A 217 PHE 0.015 0.001 PHE A 351 TYR 0.023 0.001 TYR A 264 ARG 0.004 0.000 ARG A 134 Details of bonding type rmsd hydrogen bonds : bond 0.04219 ( 272) hydrogen bonds : angle 4.16265 ( 801) SS BOND : bond 0.00615 ( 2) SS BOND : angle 0.86898 ( 4) covalent geometry : bond 0.00255 ( 3983) covalent geometry : angle 0.51248 ( 5419) *********************** 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: 22 poor density : 55 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: A 207 MET cc_start: 0.6067 (OUTLIER) cc_final: 0.5509 (tpt) REVERT: A 328 GLU cc_start: 0.6581 (tp30) cc_final: 0.6368 (tp30) REVERT: A 344 MET cc_start: 0.7082 (OUTLIER) cc_final: 0.6059 (mpp) REVERT: A 386 PHE cc_start: 0.7045 (m-10) cc_final: 0.6226 (t80) outliers start: 22 outliers final: 11 residues processed: 73 average time/residue: 0.8263 time to fit residues: 63.2923 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 : 0.419 ------------------------------------------------------------------------------- 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 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 344 MET Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 379 LEU 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: 0.9990 chunk 5 optimal weight: 0.4980 chunk 49 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 26 optimal weight: 10.0000 chunk 10 optimal weight: 0.3980 chunk 37 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3977 r_free = 0.3977 target = 0.174096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.133632 restraints weight = 4375.443| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.09 r_work: 0.3353 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 3985 Z= 0.116 Angle : 0.518 8.257 5423 Z= 0.253 Chirality : 0.037 0.126 631 Planarity : 0.004 0.025 673 Dihedral : 6.787 60.822 566 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % 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: 2.07 (0.39), residues: 492 helix: 1.64 (0.27), residues: 372 sheet: -0.06 (1.60), residues: 10 loop : 0.86 (0.67), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 213 HIS 0.002 0.000 HIS A 217 PHE 0.014 0.001 PHE A 351 TYR 0.023 0.001 TYR A 264 ARG 0.003 0.000 ARG A 134 Details of bonding type rmsd hydrogen bonds : bond 0.04068 ( 272) hydrogen bonds : angle 4.08567 ( 801) SS BOND : bond 0.00586 ( 2) SS BOND : angle 0.81770 ( 4) covalent geometry : bond 0.00246 ( 3983) covalent geometry : angle 0.51748 ( 5419) *********************** 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 72 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 57 time to evaluate : 0.409 Fit side-chains revert: symmetry clash REVERT: A 207 MET cc_start: 0.6036 (ptp) cc_final: 0.5488 (tpt) REVERT: A 328 GLU cc_start: 0.6585 (tp30) cc_final: 0.5642 (pt0) REVERT: A 386 PHE cc_start: 0.7037 (m-10) cc_final: 0.6210 (t80) outliers start: 15 outliers final: 10 residues processed: 69 average time/residue: 0.9307 time to fit residues: 67.0633 Evaluate side-chains 68 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.438 ------------------------------------------------------------------------------- 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 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 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: 0.7980 chunk 0 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 6 optimal weight: 8.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 = 0.3933 r_free = 0.3933 target = 0.169436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.128515 restraints weight = 4389.140| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.08 r_work: 0.3280 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3985 Z= 0.159 Angle : 0.564 8.090 5423 Z= 0.277 Chirality : 0.039 0.127 631 Planarity : 0.004 0.027 673 Dihedral : 6.919 65.844 566 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 3.33 % Allowed : 18.33 % 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: 1.88 (0.39), residues: 492 helix: 1.51 (0.27), residues: 368 sheet: 0.05 (1.75), residues: 10 loop : 0.75 (0.66), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP A 213 HIS 0.003 0.001 HIS A 48 PHE 0.014 0.002 PHE A 191 TYR 0.018 0.001 TYR A 264 ARG 0.003 0.000 ARG A 134 Details of bonding type rmsd hydrogen bonds : bond 0.04550 ( 272) hydrogen bonds : angle 4.23679 ( 801) SS BOND : bond 0.00957 ( 2) SS BOND : angle 0.99955 ( 4) covalent geometry : bond 0.00370 ( 3983) covalent geometry : angle 0.56325 ( 5419) *********************** 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 71 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 0.433 Fit side-chains revert: symmetry clash REVERT: A 207 MET cc_start: 0.6040 (OUTLIER) cc_final: 0.5456 (tpt) REVERT: A 386 PHE cc_start: 0.7171 (m-10) cc_final: 0.6279 (t80) outliers start: 14 outliers final: 10 residues processed: 67 average time/residue: 0.8995 time to fit residues: 63.1010 Evaluate side-chains 68 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.436 ------------------------------------------------------------------------------- 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 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 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: 1.9990 chunk 42 optimal weight: 0.9990 chunk 29 optimal weight: 10.0000 chunk 19 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.3955 r_free = 0.3955 target = 0.171381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.130652 restraints weight = 4329.445| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.05 r_work: 0.3316 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3985 Z= 0.130 Angle : 0.548 9.571 5423 Z= 0.267 Chirality : 0.038 0.127 631 Planarity : 0.004 0.027 673 Dihedral : 6.791 62.590 566 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.86 % Allowed : 18.81 % 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: 1.81 (0.39), residues: 492 helix: 1.50 (0.27), residues: 375 sheet: 0.04 (1.71), residues: 10 loop : 0.50 (0.67), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP A 213 HIS 0.002 0.001 HIS A 48 PHE 0.015 0.001 PHE A 351 TYR 0.021 0.001 TYR A 264 ARG 0.003 0.000 ARG A 134 Details of bonding type rmsd hydrogen bonds : bond 0.04240 ( 272) hydrogen bonds : angle 4.17139 ( 801) SS BOND : bond 0.00692 ( 2) SS BOND : angle 0.84453 ( 4) covalent geometry : bond 0.00289 ( 3983) covalent geometry : angle 0.54744 ( 5419) ********************** 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 73 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.397 Fit side-chains REVERT: A 207 MET cc_start: 0.6036 (OUTLIER) cc_final: 0.5480 (tpt) REVERT: A 232 LEU cc_start: 0.8279 (mp) cc_final: 0.8066 (OUTLIER) REVERT: A 314 GLN cc_start: 0.5960 (mt0) cc_final: 0.5715 (mt0) REVERT: A 328 GLU cc_start: 0.6297 (tp30) cc_final: 0.5419 (tt0) REVERT: A 386 PHE cc_start: 0.7165 (m-10) cc_final: 0.6304 (t80) outliers start: 12 outliers final: 11 residues processed: 70 average time/residue: 0.9018 time to fit residues: 65.9193 Evaluate side-chains 64 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 0.9990 chunk 1 optimal weight: 9.9990 chunk 9 optimal weight: 0.0020 chunk 39 optimal weight: 8.9990 chunk 46 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 6 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 chunk 38 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 overall best weight: 0.7794 ------------------------------------------------------------------------------- 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 = 0.3968 r_free = 0.3968 target = 0.172380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.132121 restraints weight = 4300.935| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.08 r_work: 0.3346 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3985 Z= 0.121 Angle : 0.534 8.411 5423 Z= 0.262 Chirality : 0.037 0.128 631 Planarity : 0.004 0.025 673 Dihedral : 6.682 60.466 566 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.86 % Allowed : 19.52 % 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: 1.82 (0.39), residues: 492 helix: 1.48 (0.27), residues: 383 sheet: -0.06 (1.65), residues: 10 loop : 0.56 (0.68), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP A 213 HIS 0.002 0.000 HIS A 48 PHE 0.014 0.001 PHE A 351 TYR 0.022 0.001 TYR A 264 ARG 0.003 0.000 ARG A 134 Details of bonding type rmsd hydrogen bonds : bond 0.04033 ( 272) hydrogen bonds : angle 4.08338 ( 801) SS BOND : bond 0.00568 ( 2) SS BOND : angle 0.78657 ( 4) covalent geometry : bond 0.00263 ( 3983) covalent geometry : angle 0.53390 ( 5419) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3110.53 seconds wall clock time: 54 minutes 2.39 seconds (3242.39 seconds total)