Starting phenix.real_space_refine on Sat May 10 00:39:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8de9_27388/05_2025/8de9_27388.cif Found real_map, /net/cci-nas-00/data/ceres_data/8de9_27388/05_2025/8de9_27388.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8de9_27388/05_2025/8de9_27388.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8de9_27388/05_2025/8de9_27388.map" model { file = "/net/cci-nas-00/data/ceres_data/8de9_27388/05_2025/8de9_27388.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8de9_27388/05_2025/8de9_27388.cif" } resolution = 3.4 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: 6 Type Number sf(0) Gaussians K 3 8.98 5 P 1 5.49 5 S 16 5.16 5 C 2760 2.51 5 N 626 2.21 5 O 709 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 4115 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2035 Classifications: {'peptide': 259} Link IDs: {'PTRANS': 7, 'TRANS': 251} Chain: "B" Number of atoms: 2028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2028 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 7, 'TRANS': 250} Chain: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 52 Unusual residues: {' K': 3, 'PEV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 3.27, per 1000 atoms: 0.79 Number of scatterers: 4115 At special positions: 0 Unit cell: (80.514, 97.128, 79.236, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 3 19.00 S 16 16.00 P 1 15.00 O 709 8.00 N 626 7.00 C 2760 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 93 " - pdb=" SG CYS B 93 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.15 Conformation dependent library (CDL) restraints added in 499.3 milliseconds 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 938 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 0 sheets defined 78.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 43 through 91 removed outlier: 3.569A pdb=" N ALA A 67 " --> pdb=" O THR A 63 " (cutoff:3.500A) Proline residue: A 71 - end of helix Processing helix chain 'A' and resid 95 through 113 Processing helix chain 'A' and resid 128 through 142 Processing helix chain 'A' and resid 152 through 196 removed outlier: 3.561A pdb=" N ILE A 157 " --> pdb=" O GLU A 153 " (cutoff:3.500A) Proline residue: A 168 - end of helix Processing helix chain 'A' and resid 202 through 234 removed outlier: 3.894A pdb=" N LEU A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Proline residue: A 226 - end of helix Processing helix chain 'A' and resid 237 through 250 Processing helix chain 'A' and resid 269 through 298 removed outlier: 3.702A pdb=" N ILE A 273 " --> pdb=" O TYR A 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 91 Proline residue: B 71 - end of helix Processing helix chain 'B' and resid 95 through 113 removed outlier: 3.580A pdb=" N ALA B 112 " --> pdb=" O LEU B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 142 Processing helix chain 'B' and resid 152 through 193 Proline residue: B 168 - end of helix Processing helix chain 'B' and resid 204 through 223 Processing helix chain 'B' and resid 223 through 235 removed outlier: 3.713A pdb=" N ALA B 227 " --> pdb=" O VAL B 223 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LEU B 228 " --> pdb=" O ALA B 224 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 250 Processing helix chain 'B' and resid 269 through 297 323 hydrogen bonds defined for protein. 969 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.95 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 623 1.31 - 1.44: 1184 1.44 - 1.56: 2381 1.56 - 1.69: 3 1.69 - 1.81: 26 Bond restraints: 4217 Sorted by residual: bond pdb=" CA ILE B 264 " pdb=" C ILE B 264 " ideal model delta sigma weight residual 1.530 1.584 -0.053 1.12e-02 7.97e+03 2.27e+01 bond pdb=" C31 PEV A 401 " pdb=" O2 PEV A 401 " ideal model delta sigma weight residual 1.330 1.409 -0.079 2.00e-02 2.50e+03 1.56e+01 bond pdb=" C11 PEV A 401 " pdb=" O3 PEV A 401 " ideal model delta sigma weight residual 1.335 1.398 -0.063 2.00e-02 2.50e+03 9.77e+00 bond pdb=" CA THR A 251 " pdb=" C THR A 251 " ideal model delta sigma weight residual 1.525 1.488 0.037 1.40e-02 5.10e+03 7.01e+00 bond pdb=" N THR A 251 " pdb=" CA THR A 251 " ideal model delta sigma weight residual 1.461 1.431 0.031 1.49e-02 4.50e+03 4.26e+00 ... (remaining 4212 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.27: 5583 3.27 - 6.55: 121 6.55 - 9.82: 12 9.82 - 13.09: 4 13.09 - 16.36: 1 Bond angle restraints: 5721 Sorted by residual: angle pdb=" C ILE B 264 " pdb=" CA ILE B 264 " pdb=" CB ILE B 264 " ideal model delta sigma weight residual 112.19 102.19 10.00 1.15e+00 7.56e-01 7.56e+01 angle pdb=" N GLU B 263 " pdb=" CA GLU B 263 " pdb=" C GLU B 263 " ideal model delta sigma weight residual 111.17 122.10 -10.93 1.41e+00 5.03e-01 6.01e+01 angle pdb=" C GLU B 263 " pdb=" CA GLU B 263 " pdb=" CB GLU B 263 " ideal model delta sigma weight residual 112.06 101.34 10.72 1.57e+00 4.06e-01 4.66e+01 angle pdb=" N TRP A 199 " pdb=" CA TRP A 199 " pdb=" C TRP A 199 " ideal model delta sigma weight residual 108.52 118.91 -10.39 1.63e+00 3.76e-01 4.06e+01 angle pdb=" O3P PEV A 401 " pdb=" P PEV A 401 " pdb=" O4P PEV A 401 " ideal model delta sigma weight residual 93.57 109.93 -16.36 3.00e+00 1.11e-01 2.98e+01 ... (remaining 5716 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.26: 2302 27.26 - 54.53: 105 54.53 - 81.79: 8 81.79 - 109.05: 0 109.05 - 136.32: 1 Dihedral angle restraints: 2416 sinusoidal: 947 harmonic: 1469 Sorted by residual: dihedral pdb=" CA GLN B 122 " pdb=" C GLN B 122 " pdb=" N GLU B 123 " pdb=" CA GLU B 123 " ideal model delta harmonic sigma weight residual 180.00 150.90 29.10 0 5.00e+00 4.00e-02 3.39e+01 dihedral pdb=" C3 PEV A 401 " pdb=" C1 PEV A 401 " pdb=" C2 PEV A 401 " pdb=" O3P PEV A 401 " ideal model delta sinusoidal sigma weight residual 292.80 156.48 136.32 1 3.00e+01 1.11e-03 1.84e+01 dihedral pdb=" CA LEU B 68 " pdb=" C LEU B 68 " pdb=" N GLU B 69 " pdb=" CA GLU B 69 " ideal model delta harmonic sigma weight residual -180.00 -161.10 -18.90 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 2413 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 591 0.089 - 0.178: 68 0.178 - 0.266: 5 0.266 - 0.355: 1 0.355 - 0.444: 2 Chirality restraints: 667 Sorted by residual: chirality pdb=" CA THR A 251 " pdb=" N THR A 251 " pdb=" C THR A 251 " pdb=" CB THR A 251 " both_signs ideal model delta sigma weight residual False 2.53 2.08 0.44 2.00e-01 2.50e+01 4.92e+00 chirality pdb=" CA ILE B 264 " pdb=" N ILE B 264 " pdb=" C ILE B 264 " pdb=" CB ILE B 264 " both_signs ideal model delta sigma weight residual False 2.43 2.79 -0.36 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" CA LEU A 249 " pdb=" N LEU A 249 " pdb=" C LEU A 249 " pdb=" CB LEU A 249 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.92e+00 ... (remaining 664 not shown) Planarity restraints: 685 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 119 " 0.057 5.00e-02 4.00e+02 8.76e-02 1.23e+01 pdb=" N PRO A 120 " -0.152 5.00e-02 4.00e+02 pdb=" CA PRO A 120 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 120 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 115 " -0.041 5.00e-02 4.00e+02 6.27e-02 6.28e+00 pdb=" N PRO A 116 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 116 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 116 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 196 " -0.012 2.00e-02 2.50e+03 2.34e-02 5.45e+00 pdb=" C PHE A 196 " 0.040 2.00e-02 2.50e+03 pdb=" O PHE A 196 " -0.015 2.00e-02 2.50e+03 pdb=" N VAL A 197 " -0.013 2.00e-02 2.50e+03 ... (remaining 682 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.88: 1450 2.88 - 3.44: 5034 3.44 - 4.01: 7273 4.01 - 4.57: 10264 4.57 - 5.14: 14449 Nonbonded interactions: 38470 Sorted by model distance: nonbonded pdb=" OE2 GLU A 234 " pdb=" OH TYR A 266 " model vdw 2.309 3.040 nonbonded pdb=" O PRO A 116 " pdb=" NZ LYS B 84 " model vdw 2.335 3.120 nonbonded pdb=" NZ LYS A 84 " pdb=" O PRO B 116 " model vdw 2.349 3.120 nonbonded pdb=" C ILE A 264 " pdb=" OE1 GLU A 265 " model vdw 2.376 3.270 nonbonded pdb=" OE1 GLN A 231 " pdb=" OG SER A 241 " model vdw 2.414 3.040 ... (remaining 38465 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 40 through 297) selection = chain 'B' } 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: 0.300 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.370 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 4218 Z= 0.268 Angle : 1.125 16.364 5723 Z= 0.634 Chirality : 0.059 0.444 667 Planarity : 0.008 0.088 685 Dihedral : 14.378 136.317 1475 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.23 % Allowed : 2.06 % Favored : 97.71 % 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: 2.27 (0.35), residues: 513 helix: 2.42 (0.24), residues: 392 sheet: None (None), residues: 0 loop : -1.75 (0.51), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 127 HIS 0.006 0.001 HIS B 91 PHE 0.039 0.003 PHE A 276 TYR 0.016 0.002 TYR B 284 ARG 0.003 0.000 ARG A 207 Details of bonding type rmsd hydrogen bonds : bond 0.10107 ( 323) hydrogen bonds : angle 4.66508 ( 969) SS BOND : bond 0.00323 ( 1) SS BOND : angle 0.51756 ( 2) covalent geometry : bond 0.00537 ( 4217) covalent geometry : angle 1.12476 ( 5721) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 227 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8274 (tttt) cc_final: 0.7237 (ttmm) REVERT: A 77 LYS cc_start: 0.9185 (mttm) cc_final: 0.8964 (mtpt) REVERT: A 82 GLN cc_start: 0.8363 (pt0) cc_final: 0.7630 (pp30) REVERT: A 86 ASP cc_start: 0.8291 (m-30) cc_final: 0.7641 (m-30) REVERT: A 104 LYS cc_start: 0.9424 (ttpp) cc_final: 0.9104 (ttpp) REVERT: A 105 GLN cc_start: 0.8742 (mt0) cc_final: 0.8438 (pt0) REVERT: A 195 MET cc_start: 0.8544 (tmm) cc_final: 0.7513 (tmm) REVERT: A 268 ASP cc_start: 0.7318 (t70) cc_final: 0.6974 (t0) REVERT: B 66 LYS cc_start: 0.8656 (ttpt) cc_final: 0.8149 (ttmm) REVERT: B 120 PRO cc_start: 0.8391 (Cg_endo) cc_final: 0.7369 (Cg_exo) outliers start: 1 outliers final: 0 residues processed: 227 average time/residue: 0.1899 time to fit residues: 53.1918 Evaluate side-chains 193 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 21 optimal weight: 0.0570 chunk 12 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN B 91 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.154106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.117634 restraints weight = 7199.570| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 3.89 r_work: 0.3344 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4218 Z= 0.171 Angle : 0.758 6.830 5723 Z= 0.398 Chirality : 0.045 0.178 667 Planarity : 0.005 0.041 685 Dihedral : 10.427 139.036 586 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.43 % Allowed : 15.79 % Favored : 80.78 % 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: 2.69 (0.36), residues: 513 helix: 2.64 (0.24), residues: 397 sheet: None (None), residues: 0 loop : -1.49 (0.54), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 199 HIS 0.006 0.002 HIS A 232 PHE 0.022 0.002 PHE A 158 TYR 0.017 0.002 TYR B 266 ARG 0.002 0.001 ARG A 156 Details of bonding type rmsd hydrogen bonds : bond 0.04350 ( 323) hydrogen bonds : angle 4.03216 ( 969) SS BOND : bond 0.00170 ( 1) SS BOND : angle 0.32929 ( 2) covalent geometry : bond 0.00382 ( 4217) covalent geometry : angle 0.75843 ( 5721) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 214 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8464 (tttt) cc_final: 0.7563 (ttmm) REVERT: A 70 GLN cc_start: 0.8516 (mm-40) cc_final: 0.8213 (mm110) REVERT: A 79 ARG cc_start: 0.8826 (tmt-80) cc_final: 0.8235 (tpt90) REVERT: A 82 GLN cc_start: 0.8734 (pt0) cc_final: 0.8039 (pp30) REVERT: A 83 GLU cc_start: 0.8448 (tp30) cc_final: 0.8165 (tp30) REVERT: A 86 ASP cc_start: 0.8469 (m-30) cc_final: 0.8134 (m-30) REVERT: A 95 GLN cc_start: 0.8994 (tp40) cc_final: 0.8115 (tp40) REVERT: A 101 ASP cc_start: 0.8867 (t0) cc_final: 0.8571 (t0) REVERT: A 104 LYS cc_start: 0.9486 (ttpp) cc_final: 0.9164 (ttpp) REVERT: A 180 GLN cc_start: 0.8547 (OUTLIER) cc_final: 0.8152 (tp40) REVERT: A 221 LEU cc_start: 0.9422 (tt) cc_final: 0.9207 (pp) REVERT: A 263 GLU cc_start: 0.8688 (tt0) cc_final: 0.8283 (tt0) REVERT: A 268 ASP cc_start: 0.8128 (t70) cc_final: 0.7776 (t70) REVERT: A 269 TYR cc_start: 0.8092 (m-80) cc_final: 0.7852 (m-80) REVERT: A 284 TYR cc_start: 0.8959 (t80) cc_final: 0.8623 (t80) REVERT: B 45 LYS cc_start: 0.8539 (mtmm) cc_final: 0.8167 (mmtt) REVERT: B 50 ILE cc_start: 0.8707 (OUTLIER) cc_final: 0.8320 (tt) REVERT: B 66 LYS cc_start: 0.9055 (ttpt) cc_final: 0.8177 (ttmt) REVERT: B 68 LEU cc_start: 0.9068 (mt) cc_final: 0.8853 (mp) REVERT: B 70 GLN cc_start: 0.9123 (mt0) cc_final: 0.8815 (mm-40) REVERT: B 115 ASN cc_start: 0.9310 (p0) cc_final: 0.9086 (p0) REVERT: B 122 GLN cc_start: 0.7265 (mp-120) cc_final: 0.6483 (mp10) REVERT: B 222 PHE cc_start: 0.7959 (m-80) cc_final: 0.7337 (m-10) REVERT: B 240 GLU cc_start: 0.8795 (mt-10) cc_final: 0.8519 (mt-10) REVERT: B 284 TYR cc_start: 0.9141 (t80) cc_final: 0.8870 (t80) outliers start: 15 outliers final: 6 residues processed: 218 average time/residue: 0.1661 time to fit residues: 44.3715 Evaluate side-chains 207 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 199 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 180 GLN Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain B residue 282 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 0.6980 chunk 32 optimal weight: 0.4980 chunk 48 optimal weight: 0.5980 chunk 10 optimal weight: 0.0020 chunk 42 optimal weight: 0.3980 chunk 21 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 26 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 39 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 overall best weight: 0.4188 ------------------------------------------------------------------------------- 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 = 0.4064 r_free = 0.4064 target = 0.149904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.113697 restraints weight = 7429.472| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 4.22 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4218 Z= 0.159 Angle : 0.780 11.557 5723 Z= 0.391 Chirality : 0.044 0.192 667 Planarity : 0.004 0.047 685 Dihedral : 10.330 135.336 586 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.20 % Allowed : 21.05 % Favored : 75.74 % 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: 2.55 (0.36), residues: 513 helix: 2.46 (0.24), residues: 399 sheet: None (None), residues: 0 loop : -1.27 (0.58), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 295 HIS 0.006 0.001 HIS A 232 PHE 0.022 0.001 PHE A 158 TYR 0.021 0.002 TYR A 57 ARG 0.003 0.001 ARG A 207 Details of bonding type rmsd hydrogen bonds : bond 0.04106 ( 323) hydrogen bonds : angle 3.95160 ( 969) SS BOND : bond 0.00041 ( 1) SS BOND : angle 0.35933 ( 2) covalent geometry : bond 0.00355 ( 4217) covalent geometry : angle 0.78001 ( 5721) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 206 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8308 (tttt) cc_final: 0.7520 (ttmm) REVERT: A 70 GLN cc_start: 0.8266 (mm-40) cc_final: 0.7953 (mm110) REVERT: A 79 ARG cc_start: 0.8834 (tmt-80) cc_final: 0.8342 (tpt90) REVERT: A 82 GLN cc_start: 0.8636 (pt0) cc_final: 0.7824 (pp30) REVERT: A 86 ASP cc_start: 0.8554 (m-30) cc_final: 0.7960 (m-30) REVERT: A 101 ASP cc_start: 0.8979 (t0) cc_final: 0.8663 (t0) REVERT: A 104 LYS cc_start: 0.9416 (ttpp) cc_final: 0.9126 (ttpp) REVERT: A 268 ASP cc_start: 0.8248 (t70) cc_final: 0.7743 (t0) REVERT: A 269 TYR cc_start: 0.7577 (m-80) cc_final: 0.7311 (m-80) REVERT: A 284 TYR cc_start: 0.8671 (t80) cc_final: 0.8342 (t80) REVERT: B 43 LYS cc_start: 0.7930 (tptt) cc_final: 0.7423 (tptt) REVERT: B 45 LYS cc_start: 0.8636 (mtmm) cc_final: 0.8227 (pttp) REVERT: B 48 LEU cc_start: 0.8974 (mt) cc_final: 0.8693 (mt) REVERT: B 66 LYS cc_start: 0.8952 (ttpt) cc_final: 0.8144 (ttmm) REVERT: B 68 LEU cc_start: 0.9039 (mt) cc_final: 0.8823 (mp) REVERT: B 70 GLN cc_start: 0.9084 (mt0) cc_final: 0.8687 (mm-40) REVERT: B 115 ASN cc_start: 0.9310 (p0) cc_final: 0.9089 (p0) REVERT: B 158 PHE cc_start: 0.9161 (t80) cc_final: 0.8888 (t80) REVERT: B 222 PHE cc_start: 0.8064 (m-80) cc_final: 0.7834 (m-10) REVERT: B 240 GLU cc_start: 0.8636 (mt-10) cc_final: 0.8261 (mt-10) REVERT: B 295 TRP cc_start: 0.7906 (OUTLIER) cc_final: 0.7283 (m100) outliers start: 14 outliers final: 7 residues processed: 209 average time/residue: 0.1663 time to fit residues: 42.1040 Evaluate side-chains 204 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 196 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 295 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 37 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 12 optimal weight: 0.3980 chunk 5 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 HIS A 180 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.150374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.116349 restraints weight = 7349.551| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 3.70 r_work: 0.3320 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4218 Z= 0.169 Angle : 0.780 9.456 5723 Z= 0.397 Chirality : 0.043 0.163 667 Planarity : 0.004 0.039 685 Dihedral : 10.205 132.399 586 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.75 % Allowed : 23.11 % Favored : 74.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.49 (0.36), residues: 513 helix: 2.41 (0.25), residues: 399 sheet: None (None), residues: 0 loop : -1.22 (0.56), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 295 HIS 0.001 0.000 HIS B 151 PHE 0.021 0.001 PHE A 158 TYR 0.022 0.002 TYR A 162 ARG 0.009 0.001 ARG A 207 Details of bonding type rmsd hydrogen bonds : bond 0.04297 ( 323) hydrogen bonds : angle 3.87463 ( 969) SS BOND : bond 0.00210 ( 1) SS BOND : angle 0.15156 ( 2) covalent geometry : bond 0.00393 ( 4217) covalent geometry : angle 0.77968 ( 5721) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 193 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8584 (tttt) cc_final: 0.7797 (ttmm) REVERT: A 70 GLN cc_start: 0.8579 (mm110) cc_final: 0.8243 (mm110) REVERT: A 82 GLN cc_start: 0.8670 (pt0) cc_final: 0.7807 (pp30) REVERT: A 83 GLU cc_start: 0.8619 (tp30) cc_final: 0.8246 (tp30) REVERT: A 86 ASP cc_start: 0.8544 (m-30) cc_final: 0.8019 (m-30) REVERT: A 104 LYS cc_start: 0.9483 (ttpp) cc_final: 0.9240 (ttpp) REVERT: A 162 TYR cc_start: 0.9057 (t80) cc_final: 0.8822 (t80) REVERT: A 284 TYR cc_start: 0.9081 (t80) cc_final: 0.8842 (t80) REVERT: B 43 LYS cc_start: 0.8167 (tptt) cc_final: 0.7644 (tptt) REVERT: B 45 LYS cc_start: 0.8710 (mtmm) cc_final: 0.8331 (pttp) REVERT: B 48 LEU cc_start: 0.9028 (mt) cc_final: 0.8711 (mt) REVERT: B 51 PHE cc_start: 0.9266 (t80) cc_final: 0.9033 (t80) REVERT: B 66 LYS cc_start: 0.9049 (ttpt) cc_final: 0.8738 (ttpp) REVERT: B 70 GLN cc_start: 0.9226 (mt0) cc_final: 0.8981 (mm-40) REVERT: B 86 ASP cc_start: 0.9008 (p0) cc_final: 0.8747 (p0) REVERT: B 104 LYS cc_start: 0.9460 (ttmm) cc_final: 0.9135 (mtmm) REVERT: B 158 PHE cc_start: 0.9273 (t80) cc_final: 0.9062 (t80) REVERT: B 180 GLN cc_start: 0.8992 (tt0) cc_final: 0.8457 (tp-100) REVERT: B 195 MET cc_start: 0.7566 (mmm) cc_final: 0.7205 (mpp) REVERT: B 222 PHE cc_start: 0.8032 (m-80) cc_final: 0.7807 (m-80) REVERT: B 240 GLU cc_start: 0.8853 (mt-10) cc_final: 0.8535 (mt-10) REVERT: B 250 THR cc_start: 0.9388 (OUTLIER) cc_final: 0.9178 (p) REVERT: B 282 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8412 (tp) REVERT: B 291 MET cc_start: 0.8702 (tmm) cc_final: 0.7953 (mmp) outliers start: 12 outliers final: 6 residues processed: 197 average time/residue: 0.1712 time to fit residues: 40.8975 Evaluate side-chains 202 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 194 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 180 GLN Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 282 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 45 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 46 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.144553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.110576 restraints weight = 7666.309| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 4.10 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.4346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4218 Z= 0.170 Angle : 0.781 11.246 5723 Z= 0.395 Chirality : 0.043 0.168 667 Planarity : 0.004 0.046 685 Dihedral : 10.155 130.279 586 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.66 % Allowed : 25.63 % Favored : 70.71 % 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: 2.35 (0.36), residues: 513 helix: 2.30 (0.24), residues: 399 sheet: None (None), residues: 0 loop : -1.25 (0.57), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 295 HIS 0.002 0.001 HIS A 91 PHE 0.017 0.001 PHE A 158 TYR 0.020 0.002 TYR A 162 ARG 0.003 0.000 ARG A 207 Details of bonding type rmsd hydrogen bonds : bond 0.04229 ( 323) hydrogen bonds : angle 3.90177 ( 969) SS BOND : bond 0.00082 ( 1) SS BOND : angle 0.12944 ( 2) covalent geometry : bond 0.00395 ( 4217) covalent geometry : angle 0.78111 ( 5721) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 203 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8445 (tttt) cc_final: 0.7612 (ttmm) REVERT: A 70 GLN cc_start: 0.8315 (mm110) cc_final: 0.7782 (mm110) REVERT: A 82 GLN cc_start: 0.8632 (pt0) cc_final: 0.7801 (pp30) REVERT: A 83 GLU cc_start: 0.8708 (tp30) cc_final: 0.8212 (tp30) REVERT: A 86 ASP cc_start: 0.8590 (m-30) cc_final: 0.8128 (m-30) REVERT: A 104 LYS cc_start: 0.9449 (ttpp) cc_final: 0.9209 (ttpp) REVERT: A 263 GLU cc_start: 0.8689 (tt0) cc_final: 0.8317 (tm-30) REVERT: A 268 ASP cc_start: 0.8246 (t0) cc_final: 0.7419 (t70) REVERT: A 284 TYR cc_start: 0.8786 (t80) cc_final: 0.8508 (t80) REVERT: B 43 LYS cc_start: 0.8031 (tptt) cc_final: 0.7727 (tptt) REVERT: B 45 LYS cc_start: 0.8734 (mtmm) cc_final: 0.8399 (pttp) REVERT: B 48 LEU cc_start: 0.9026 (mt) cc_final: 0.8744 (mt) REVERT: B 66 LYS cc_start: 0.8987 (ttpt) cc_final: 0.8601 (ttpp) REVERT: B 70 GLN cc_start: 0.9182 (mt0) cc_final: 0.8838 (mm-40) REVERT: B 83 GLU cc_start: 0.8707 (pp20) cc_final: 0.8452 (pp20) REVERT: B 86 ASP cc_start: 0.8968 (p0) cc_final: 0.8605 (p0) REVERT: B 100 GLU cc_start: 0.9075 (mm-30) cc_final: 0.8493 (tp30) REVERT: B 104 LYS cc_start: 0.9384 (ttmm) cc_final: 0.9065 (mtmm) REVERT: B 158 PHE cc_start: 0.9193 (t80) cc_final: 0.8963 (t80) REVERT: B 240 GLU cc_start: 0.8694 (mt-10) cc_final: 0.8312 (mt-10) REVERT: B 250 THR cc_start: 0.9211 (OUTLIER) cc_final: 0.8952 (p) REVERT: B 282 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8145 (tp) REVERT: B 291 MET cc_start: 0.8410 (tmm) cc_final: 0.7797 (mmp) outliers start: 16 outliers final: 12 residues processed: 206 average time/residue: 0.1681 time to fit residues: 42.0368 Evaluate side-chains 205 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 191 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 282 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 41 optimal weight: 0.0050 chunk 43 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 12 optimal weight: 0.4980 chunk 35 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 16 optimal weight: 0.0770 chunk 39 optimal weight: 5.9990 chunk 6 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 overall best weight: 0.3752 ------------------------------------------------------------------------------- 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 = 0.4038 r_free = 0.4038 target = 0.147317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.113802 restraints weight = 7526.840| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 4.07 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.4700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4218 Z= 0.162 Angle : 0.837 11.813 5723 Z= 0.414 Chirality : 0.044 0.170 667 Planarity : 0.004 0.044 685 Dihedral : 10.053 127.610 586 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.20 % Allowed : 29.75 % Favored : 67.05 % 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: 2.19 (0.36), residues: 513 helix: 2.21 (0.25), residues: 399 sheet: None (None), residues: 0 loop : -1.42 (0.56), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 295 HIS 0.002 0.000 HIS A 91 PHE 0.020 0.001 PHE A 158 TYR 0.022 0.002 TYR A 162 ARG 0.003 0.000 ARG A 79 Details of bonding type rmsd hydrogen bonds : bond 0.04192 ( 323) hydrogen bonds : angle 3.91358 ( 969) SS BOND : bond 0.00041 ( 1) SS BOND : angle 0.10982 ( 2) covalent geometry : bond 0.00364 ( 4217) covalent geometry : angle 0.83720 ( 5721) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 200 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8412 (tttt) cc_final: 0.7536 (ttmm) REVERT: A 70 GLN cc_start: 0.8304 (mm110) cc_final: 0.7887 (mm110) REVERT: A 82 GLN cc_start: 0.8661 (pt0) cc_final: 0.7778 (pp30) REVERT: A 83 GLU cc_start: 0.8570 (tp30) cc_final: 0.8174 (tp30) REVERT: A 86 ASP cc_start: 0.8591 (m-30) cc_final: 0.8128 (m-30) REVERT: A 104 LYS cc_start: 0.9434 (ttpp) cc_final: 0.9190 (ttpp) REVERT: A 263 GLU cc_start: 0.8768 (tt0) cc_final: 0.8347 (tm-30) REVERT: A 268 ASP cc_start: 0.8205 (OUTLIER) cc_final: 0.7724 (t70) REVERT: A 269 TYR cc_start: 0.7743 (m-80) cc_final: 0.7513 (m-80) REVERT: A 284 TYR cc_start: 0.8736 (t80) cc_final: 0.8460 (t80) REVERT: B 43 LYS cc_start: 0.8080 (tptt) cc_final: 0.7256 (tptt) REVERT: B 45 LYS cc_start: 0.8753 (mtmm) cc_final: 0.8234 (pttt) REVERT: B 48 LEU cc_start: 0.8940 (mt) cc_final: 0.8642 (mt) REVERT: B 66 LYS cc_start: 0.8913 (ttpt) cc_final: 0.8661 (ttpp) REVERT: B 70 GLN cc_start: 0.9171 (mt0) cc_final: 0.8805 (mm-40) REVERT: B 86 ASP cc_start: 0.9042 (p0) cc_final: 0.8718 (p0) REVERT: B 104 LYS cc_start: 0.9364 (ttmm) cc_final: 0.9039 (mtmm) REVERT: B 240 GLU cc_start: 0.8675 (mt-10) cc_final: 0.8302 (mt-10) REVERT: B 250 THR cc_start: 0.9144 (OUTLIER) cc_final: 0.8899 (p) outliers start: 14 outliers final: 9 residues processed: 203 average time/residue: 0.1700 time to fit residues: 41.8689 Evaluate side-chains 206 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 195 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 250 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 35 optimal weight: 0.5980 chunk 30 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 1 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 = 0.3994 r_free = 0.3994 target = 0.144553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.110515 restraints weight = 7655.411| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 4.15 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.4857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4218 Z= 0.187 Angle : 0.900 12.156 5723 Z= 0.445 Chirality : 0.045 0.169 667 Planarity : 0.004 0.044 685 Dihedral : 10.027 126.117 586 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 4.12 % Allowed : 30.21 % Favored : 65.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.36), residues: 513 helix: 2.16 (0.25), residues: 397 sheet: None (None), residues: 0 loop : -1.54 (0.55), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 199 HIS 0.002 0.001 HIS B 232 PHE 0.019 0.001 PHE B 51 TYR 0.019 0.002 TYR A 162 ARG 0.010 0.001 ARG A 79 Details of bonding type rmsd hydrogen bonds : bond 0.04356 ( 323) hydrogen bonds : angle 3.99116 ( 969) SS BOND : bond 0.00051 ( 1) SS BOND : angle 0.21470 ( 2) covalent geometry : bond 0.00445 ( 4217) covalent geometry : angle 0.89965 ( 5721) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 199 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8256 (mmtt) cc_final: 0.7985 (mmtm) REVERT: A 66 LYS cc_start: 0.8494 (tttt) cc_final: 0.7648 (ttmm) REVERT: A 70 GLN cc_start: 0.8323 (mm110) cc_final: 0.7862 (mm110) REVERT: A 82 GLN cc_start: 0.8587 (pt0) cc_final: 0.7761 (pp30) REVERT: A 83 GLU cc_start: 0.8511 (tp30) cc_final: 0.8010 (tp30) REVERT: A 86 ASP cc_start: 0.8592 (m-30) cc_final: 0.8112 (m-30) REVERT: A 179 ASP cc_start: 0.8562 (t0) cc_final: 0.8318 (t0) REVERT: A 263 GLU cc_start: 0.8765 (tt0) cc_final: 0.8423 (tm-30) REVERT: A 268 ASP cc_start: 0.8416 (OUTLIER) cc_final: 0.7697 (p0) REVERT: A 284 TYR cc_start: 0.8783 (t80) cc_final: 0.8514 (t80) REVERT: B 43 LYS cc_start: 0.8055 (tptt) cc_final: 0.7541 (tptt) REVERT: B 45 LYS cc_start: 0.8759 (mtmm) cc_final: 0.8254 (pttt) REVERT: B 48 LEU cc_start: 0.9006 (mt) cc_final: 0.8759 (mt) REVERT: B 66 LYS cc_start: 0.9001 (ttpt) cc_final: 0.8721 (ttpp) REVERT: B 70 GLN cc_start: 0.9190 (mt0) cc_final: 0.8843 (mm-40) REVERT: B 86 ASP cc_start: 0.8936 (p0) cc_final: 0.8557 (p0) REVERT: B 104 LYS cc_start: 0.9354 (ttmm) cc_final: 0.9010 (mtmm) REVERT: B 222 PHE cc_start: 0.8041 (m-10) cc_final: 0.7680 (m-10) REVERT: B 240 GLU cc_start: 0.8699 (mt-10) cc_final: 0.8312 (mt-10) REVERT: B 250 THR cc_start: 0.9219 (OUTLIER) cc_final: 0.8972 (p) REVERT: B 291 MET cc_start: 0.8715 (tmm) cc_final: 0.7790 (mmp) outliers start: 18 outliers final: 11 residues processed: 205 average time/residue: 0.1720 time to fit residues: 42.8531 Evaluate side-chains 201 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 188 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 250 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 20 optimal weight: 0.4980 chunk 3 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 8 optimal weight: 0.0170 chunk 22 optimal weight: 2.9990 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 HIS B 122 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.146120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.111027 restraints weight = 7479.128| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 4.20 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.5077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4218 Z= 0.179 Angle : 0.948 12.410 5723 Z= 0.469 Chirality : 0.046 0.189 667 Planarity : 0.004 0.052 685 Dihedral : 9.925 123.760 586 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.75 % Allowed : 32.04 % Favored : 65.22 % 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: 1.99 (0.36), residues: 513 helix: 2.15 (0.25), residues: 396 sheet: None (None), residues: 0 loop : -1.72 (0.54), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 295 HIS 0.009 0.001 HIS A 232 PHE 0.020 0.001 PHE B 51 TYR 0.016 0.002 TYR A 162 ARG 0.003 0.000 ARG A 79 Details of bonding type rmsd hydrogen bonds : bond 0.04419 ( 323) hydrogen bonds : angle 4.07731 ( 969) SS BOND : bond 0.00040 ( 1) SS BOND : angle 0.12638 ( 2) covalent geometry : bond 0.00412 ( 4217) covalent geometry : angle 0.94841 ( 5721) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 205 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8210 (mmtt) cc_final: 0.7963 (mmtm) REVERT: A 66 LYS cc_start: 0.8451 (tttt) cc_final: 0.7640 (ttmt) REVERT: A 70 GLN cc_start: 0.8335 (mm110) cc_final: 0.7838 (mm110) REVERT: A 82 GLN cc_start: 0.8627 (pt0) cc_final: 0.7809 (pp30) REVERT: A 83 GLU cc_start: 0.8500 (tp30) cc_final: 0.8159 (tp30) REVERT: A 86 ASP cc_start: 0.8574 (m-30) cc_final: 0.8107 (m-30) REVERT: A 158 PHE cc_start: 0.9180 (t80) cc_final: 0.8946 (t80) REVERT: A 179 ASP cc_start: 0.8608 (t0) cc_final: 0.8368 (t0) REVERT: A 263 GLU cc_start: 0.8845 (tt0) cc_final: 0.8380 (tm-30) REVERT: A 268 ASP cc_start: 0.8152 (OUTLIER) cc_final: 0.7947 (p0) REVERT: A 284 TYR cc_start: 0.8744 (t80) cc_final: 0.8473 (t80) REVERT: B 43 LYS cc_start: 0.8102 (tptt) cc_final: 0.7546 (tptt) REVERT: B 45 LYS cc_start: 0.8814 (mtmm) cc_final: 0.8350 (pttt) REVERT: B 66 LYS cc_start: 0.8949 (ttpt) cc_final: 0.8033 (ttmt) REVERT: B 70 GLN cc_start: 0.9184 (mt0) cc_final: 0.8767 (mm-40) REVERT: B 86 ASP cc_start: 0.9011 (p0) cc_final: 0.8638 (p0) REVERT: B 104 LYS cc_start: 0.9305 (ttmm) cc_final: 0.9037 (mtmm) REVERT: B 222 PHE cc_start: 0.8045 (m-10) cc_final: 0.7667 (m-10) REVERT: B 240 GLU cc_start: 0.8668 (mt-10) cc_final: 0.8289 (mt-10) REVERT: B 250 THR cc_start: 0.9157 (OUTLIER) cc_final: 0.8916 (p) REVERT: B 291 MET cc_start: 0.8669 (tmm) cc_final: 0.7769 (mmp) outliers start: 12 outliers final: 8 residues processed: 207 average time/residue: 0.1748 time to fit residues: 43.8847 Evaluate side-chains 196 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 186 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 250 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 18 optimal weight: 0.4980 chunk 45 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4012 r_free = 0.4012 target = 0.145233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.110108 restraints weight = 7525.441| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 4.12 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.5150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4218 Z= 0.187 Angle : 0.979 12.985 5723 Z= 0.479 Chirality : 0.048 0.295 667 Planarity : 0.004 0.042 685 Dihedral : 9.803 121.373 586 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.97 % Allowed : 32.49 % Favored : 64.53 % 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: 1.90 (0.37), residues: 513 helix: 2.09 (0.25), residues: 397 sheet: None (None), residues: 0 loop : -1.80 (0.54), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 295 HIS 0.002 0.000 HIS B 151 PHE 0.021 0.001 PHE B 51 TYR 0.023 0.002 TYR B 57 ARG 0.006 0.001 ARG A 207 Details of bonding type rmsd hydrogen bonds : bond 0.04479 ( 323) hydrogen bonds : angle 4.09519 ( 969) SS BOND : bond 0.00035 ( 1) SS BOND : angle 0.24057 ( 2) covalent geometry : bond 0.00439 ( 4217) covalent geometry : angle 0.97949 ( 5721) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 203 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8112 (mmtt) cc_final: 0.7883 (mmtm) REVERT: A 66 LYS cc_start: 0.8509 (tttt) cc_final: 0.7645 (ttmm) REVERT: A 70 GLN cc_start: 0.8353 (mm110) cc_final: 0.7848 (mm110) REVERT: A 82 GLN cc_start: 0.8606 (pt0) cc_final: 0.7895 (pp30) REVERT: A 83 GLU cc_start: 0.8387 (tp30) cc_final: 0.7899 (tp30) REVERT: A 86 ASP cc_start: 0.8599 (m-30) cc_final: 0.7935 (m-30) REVERT: A 158 PHE cc_start: 0.9247 (t80) cc_final: 0.9034 (t80) REVERT: A 179 ASP cc_start: 0.8590 (t0) cc_final: 0.8340 (t0) REVERT: A 240 GLU cc_start: 0.8356 (mt-10) cc_final: 0.7772 (pt0) REVERT: A 271 LYS cc_start: 0.8518 (mmtm) cc_final: 0.8268 (mmmt) REVERT: A 284 TYR cc_start: 0.8796 (t80) cc_final: 0.8525 (t80) REVERT: B 43 LYS cc_start: 0.8055 (tptt) cc_final: 0.7497 (tptt) REVERT: B 45 LYS cc_start: 0.8822 (mtmm) cc_final: 0.8366 (pttt) REVERT: B 66 LYS cc_start: 0.8987 (ttpt) cc_final: 0.8713 (ttpp) REVERT: B 70 GLN cc_start: 0.9164 (mt0) cc_final: 0.8814 (mm-40) REVERT: B 222 PHE cc_start: 0.8119 (m-10) cc_final: 0.7750 (m-10) REVERT: B 240 GLU cc_start: 0.8685 (mt-10) cc_final: 0.8296 (mt-10) REVERT: B 250 THR cc_start: 0.9200 (OUTLIER) cc_final: 0.8958 (p) REVERT: B 291 MET cc_start: 0.8666 (tmm) cc_final: 0.7852 (mmp) outliers start: 13 outliers final: 9 residues processed: 206 average time/residue: 0.1709 time to fit residues: 42.5484 Evaluate side-chains 192 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 182 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 250 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 1 optimal weight: 0.0770 chunk 49 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 chunk 41 optimal weight: 8.9990 chunk 46 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 overall best weight: 0.6338 ------------------------------------------------------------------------------- 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 = 0.4008 r_free = 0.4008 target = 0.144849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.109096 restraints weight = 7543.110| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 4.28 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.5333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 4218 Z= 0.192 Angle : 1.025 12.628 5723 Z= 0.505 Chirality : 0.048 0.348 667 Planarity : 0.005 0.042 685 Dihedral : 9.719 119.044 586 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.52 % Allowed : 35.01 % Favored : 62.47 % 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: 1.83 (0.36), residues: 513 helix: 2.02 (0.25), residues: 397 sheet: None (None), residues: 0 loop : -1.72 (0.55), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 295 HIS 0.002 0.001 HIS B 151 PHE 0.020 0.001 PHE B 51 TYR 0.021 0.002 TYR B 57 ARG 0.002 0.000 ARG A 79 Details of bonding type rmsd hydrogen bonds : bond 0.04482 ( 323) hydrogen bonds : angle 4.17249 ( 969) SS BOND : bond 0.00018 ( 1) SS BOND : angle 0.13082 ( 2) covalent geometry : bond 0.00452 ( 4217) covalent geometry : angle 1.02506 ( 5721) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 194 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8146 (mmtt) cc_final: 0.7937 (mmtm) REVERT: A 66 LYS cc_start: 0.8514 (tttt) cc_final: 0.7637 (ttmm) REVERT: A 70 GLN cc_start: 0.8369 (mm110) cc_final: 0.7865 (mm110) REVERT: A 82 GLN cc_start: 0.8624 (pt0) cc_final: 0.7795 (pp30) REVERT: A 83 GLU cc_start: 0.8321 (tp30) cc_final: 0.8000 (tp30) REVERT: A 86 ASP cc_start: 0.8555 (m-30) cc_final: 0.8048 (m-30) REVERT: A 179 ASP cc_start: 0.8584 (t0) cc_final: 0.8337 (t0) REVERT: A 207 ARG cc_start: 0.8848 (mpp80) cc_final: 0.8626 (mpp80) REVERT: A 240 GLU cc_start: 0.8428 (mt-10) cc_final: 0.7831 (pt0) REVERT: A 263 GLU cc_start: 0.8696 (tm-30) cc_final: 0.8415 (tm-30) REVERT: A 284 TYR cc_start: 0.8817 (t80) cc_final: 0.8553 (t80) REVERT: B 66 LYS cc_start: 0.9022 (ttpt) cc_final: 0.8062 (ttmt) REVERT: B 70 GLN cc_start: 0.9171 (mt0) cc_final: 0.8725 (mm-40) REVERT: B 179 ASP cc_start: 0.9061 (t0) cc_final: 0.8718 (t0) REVERT: B 222 PHE cc_start: 0.8113 (m-10) cc_final: 0.7756 (m-10) REVERT: B 240 GLU cc_start: 0.8670 (mt-10) cc_final: 0.8270 (mt-10) REVERT: B 250 THR cc_start: 0.9207 (OUTLIER) cc_final: 0.8969 (p) REVERT: B 291 MET cc_start: 0.8638 (tmm) cc_final: 0.7974 (mmp) outliers start: 11 outliers final: 9 residues processed: 197 average time/residue: 0.1972 time to fit residues: 48.3539 Evaluate side-chains 190 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 180 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 250 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 9 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 22 optimal weight: 8.9990 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 = 0.4157 r_free = 0.4157 target = 0.152763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.117438 restraints weight = 7286.531| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 3.70 r_work: 0.3387 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.5338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 4218 Z= 0.198 Angle : 1.036 15.947 5723 Z= 0.510 Chirality : 0.049 0.352 667 Planarity : 0.005 0.040 685 Dihedral : 9.705 117.668 586 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.29 % Allowed : 35.24 % Favored : 62.47 % 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: 1.73 (0.36), residues: 513 helix: 1.99 (0.25), residues: 397 sheet: None (None), residues: 0 loop : -1.95 (0.53), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 295 HIS 0.002 0.001 HIS B 151 PHE 0.024 0.001 PHE A 158 TYR 0.022 0.002 TYR B 57 ARG 0.007 0.001 ARG A 79 Details of bonding type rmsd hydrogen bonds : bond 0.04527 ( 323) hydrogen bonds : angle 4.19336 ( 969) SS BOND : bond 0.00028 ( 1) SS BOND : angle 0.14957 ( 2) covalent geometry : bond 0.00470 ( 4217) covalent geometry : angle 1.03619 ( 5721) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2287.79 seconds wall clock time: 40 minutes 23.13 seconds (2423.13 seconds total)