Starting phenix.real_space_refine on Mon Feb 10 22:54:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qd0_18339/02_2025/8qd0_18339.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qd0_18339/02_2025/8qd0_18339.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qd0_18339/02_2025/8qd0_18339.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qd0_18339/02_2025/8qd0_18339.map" model { file = "/net/cci-nas-00/data/ceres_data/8qd0_18339/02_2025/8qd0_18339.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qd0_18339/02_2025/8qd0_18339.cif" } resolution = 2.8 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= 0.098 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 19 5.16 5 C 2187 2.51 5 N 522 2.21 5 O 562 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 3290 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3283 Classifications: {'peptide': 422} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 406} Chain breaks: 1 Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'CHT': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.49, per 1000 atoms: 0.76 Number of scatterers: 3290 At special positions: 0 Unit cell: (83.658, 56.154, 65.322, 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 19 16.00 O 562 8.00 N 522 7.00 C 2187 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 374.5 milliseconds 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 772 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 0 sheets defined 91.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 82 through 107 removed outlier: 4.255A pdb=" N ALA A 86 " --> pdb=" O ARG A 82 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N TYR A 105 " --> pdb=" O GLN A 101 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLY A 106 " --> pdb=" O TRP A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 117 removed outlier: 4.096A pdb=" N HIS A 114 " --> pdb=" O ASN A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 168 removed outlier: 3.922A pdb=" N ILE A 123 " --> pdb=" O SER A 119 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TRP A 125 " --> pdb=" O PHE A 121 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU A 126 " --> pdb=" O ALA A 122 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER A 127 " --> pdb=" O ILE A 123 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N TYR A 130 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N MET A 131 " --> pdb=" O SER A 127 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE A 135 " --> pdb=" O MET A 131 " (cutoff:3.500A) Proline residue: A 136 - end of helix removed outlier: 5.138A pdb=" N LEU A 139 " --> pdb=" O ILE A 135 " (cutoff:3.500A) Proline residue: A 140 - end of helix removed outlier: 7.574A pdb=" N LEU A 150 " --> pdb=" O GLU A 146 " (cutoff:3.500A) removed outlier: 8.799A pdb=" N ARG A 151 " --> pdb=" O LYS A 147 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N THR A 152 " --> pdb=" O PHE A 148 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE A 153 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 172 Processing helix chain 'A' and resid 176 through 193 removed outlier: 3.646A pdb=" N THR A 180 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N VAL A 192 " --> pdb=" O SER A 188 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N PHE A 193 " --> pdb=" O VAL A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 206 removed outlier: 3.557A pdb=" N ILE A 201 " --> pdb=" O MET A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 237 Proline residue: A 233 - end of helix Processing helix chain 'A' and resid 242 through 272 Processing helix chain 'A' and resid 281 through 291 Processing helix chain 'A' and resid 296 through 305 removed outlier: 3.789A pdb=" N PHE A 305 " --> pdb=" O ILE A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 330 removed outlier: 3.552A pdb=" N ALA A 323 " --> pdb=" O LEU A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 339 removed outlier: 3.526A pdb=" N MET A 334 " --> pdb=" O LEU A 330 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TRP A 337 " --> pdb=" O ARG A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 372 Processing helix chain 'A' and resid 373 through 396 Processing helix chain 'A' and resid 400 through 431 removed outlier: 3.653A pdb=" N PHE A 414 " --> pdb=" O THR A 410 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY A 417 " --> pdb=" O PHE A 413 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU A 419 " --> pdb=" O MET A 415 " (cutoff:3.500A) Proline residue: A 420 - end of helix removed outlier: 3.815A pdb=" N PHE A 423 " --> pdb=" O LEU A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 465 removed outlier: 3.609A pdb=" N SER A 438 " --> pdb=" O SER A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 486 removed outlier: 3.694A pdb=" N GLY A 469 " --> pdb=" O GLY A 465 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE A 486 " --> pdb=" O ALA A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 502 271 hydrogen bonds defined for protein. 810 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: 0.91 Time building geometry restraints manager: 0.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 608 1.33 - 1.45: 840 1.45 - 1.57: 1892 1.57 - 1.69: 0 1.69 - 1.81: 31 Bond restraints: 3371 Sorted by residual: bond pdb=" N LEU A 441 " pdb=" CA LEU A 441 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.23e-02 6.61e+03 1.01e+01 bond pdb=" N PRO A 276 " pdb=" CA PRO A 276 " ideal model delta sigma weight residual 1.467 1.434 0.033 1.24e-02 6.50e+03 7.16e+00 bond pdb=" N GLU A 435 " pdb=" CA GLU A 435 " ideal model delta sigma weight residual 1.459 1.486 -0.028 1.25e-02 6.40e+03 4.92e+00 bond pdb=" C LEU A 441 " pdb=" O LEU A 441 " ideal model delta sigma weight residual 1.237 1.215 0.021 1.19e-02 7.06e+03 3.25e+00 bond pdb=" C PRO A 276 " pdb=" O PRO A 276 " ideal model delta sigma weight residual 1.233 1.211 0.022 1.24e-02 6.50e+03 3.08e+00 ... (remaining 3366 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 4471 1.74 - 3.48: 94 3.48 - 5.22: 18 5.22 - 6.96: 5 6.96 - 8.71: 2 Bond angle restraints: 4590 Sorted by residual: angle pdb=" CA PRO A 198 " pdb=" N PRO A 198 " pdb=" CD PRO A 198 " ideal model delta sigma weight residual 112.00 106.44 5.56 1.40e+00 5.10e-01 1.58e+01 angle pdb=" C PRO A 276 " pdb=" CA PRO A 276 " pdb=" CB PRO A 276 " ideal model delta sigma weight residual 111.40 106.40 5.00 1.54e+00 4.22e-01 1.05e+01 angle pdb=" N VAL A 237 " pdb=" CA VAL A 237 " pdb=" C VAL A 237 " ideal model delta sigma weight residual 108.15 111.20 -3.05 9.90e-01 1.02e+00 9.47e+00 angle pdb=" N PRO A 198 " pdb=" CD PRO A 198 " pdb=" CG PRO A 198 " ideal model delta sigma weight residual 103.20 98.66 4.54 1.50e+00 4.44e-01 9.16e+00 angle pdb=" N LEU A 441 " pdb=" CA LEU A 441 " pdb=" C LEU A 441 " ideal model delta sigma weight residual 111.36 108.09 3.27 1.09e+00 8.42e-01 9.00e+00 ... (remaining 4585 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.49: 1725 17.49 - 34.99: 159 34.99 - 52.48: 45 52.48 - 69.97: 5 69.97 - 87.47: 5 Dihedral angle restraints: 1939 sinusoidal: 728 harmonic: 1211 Sorted by residual: dihedral pdb=" CA MET A 197 " pdb=" C MET A 197 " pdb=" N PRO A 198 " pdb=" CA PRO A 198 " ideal model delta harmonic sigma weight residual 180.00 159.03 20.97 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CD ARG A 333 " pdb=" NE ARG A 333 " pdb=" CZ ARG A 333 " pdb=" NH1 ARG A 333 " ideal model delta sinusoidal sigma weight residual 0.00 -30.26 30.26 1 1.00e+01 1.00e-02 1.31e+01 dihedral pdb=" CA ASN A 320 " pdb=" CB ASN A 320 " pdb=" CG ASN A 320 " pdb=" OD1 ASN A 320 " ideal model delta sinusoidal sigma weight residual 120.00 -166.69 -73.31 2 2.00e+01 2.50e-03 1.10e+01 ... (remaining 1936 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 427 0.046 - 0.092: 101 0.092 - 0.138: 14 0.138 - 0.184: 0 0.184 - 0.230: 1 Chirality restraints: 543 Sorted by residual: chirality pdb=" CB ILE A 108 " pdb=" CA ILE A 108 " pdb=" CG1 ILE A 108 " pdb=" CG2 ILE A 108 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CA ARG A 333 " pdb=" N ARG A 333 " pdb=" C ARG A 333 " pdb=" CB ARG A 333 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.69e-01 chirality pdb=" CA PRO A 432 " pdb=" N PRO A 432 " pdb=" C PRO A 432 " pdb=" CB PRO A 432 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.11 2.00e-01 2.50e+01 3.25e-01 ... (remaining 540 not shown) Planarity restraints: 555 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 333 " 0.563 9.50e-02 1.11e+02 2.52e-01 3.89e+01 pdb=" NE ARG A 333 " -0.032 2.00e-02 2.50e+03 pdb=" CZ ARG A 333 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG A 333 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 333 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 197 " 0.065 5.00e-02 4.00e+02 9.54e-02 1.46e+01 pdb=" N PRO A 198 " -0.165 5.00e-02 4.00e+02 pdb=" CA PRO A 198 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 198 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 143 " 0.009 2.00e-02 2.50e+03 1.02e-02 2.60e+00 pdb=" CG TRP A 143 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TRP A 143 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP A 143 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 143 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 143 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 143 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 143 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 143 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 143 " 0.000 2.00e-02 2.50e+03 ... (remaining 552 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 1160 2.85 - 3.36: 3528 3.36 - 3.87: 5734 3.87 - 4.39: 6688 4.39 - 4.90: 11284 Nonbonded interactions: 28394 Sorted by model distance: nonbonded pdb=" OE1 GLN A 101 " pdb=" NZ LYS A 168 " model vdw 2.337 3.120 nonbonded pdb=" OE1 GLU A 342 " pdb=" ND2 ASN A 345 " model vdw 2.371 3.120 nonbonded pdb=" O VAL A 391 " pdb=" OG1 THR A 395 " model vdw 2.444 3.040 nonbonded pdb=" NH2 ARG A 151 " pdb=" O ILE A 269 " model vdw 2.459 3.120 nonbonded pdb=" O ILE A 452 " pdb=" OG SER A 456 " model vdw 2.483 3.040 ... (remaining 28389 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: 0.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.660 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 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 0.039 3371 Z= 0.197 Angle : 0.634 8.706 4590 Z= 0.358 Chirality : 0.038 0.230 543 Planarity : 0.012 0.252 555 Dihedral : 15.295 87.467 1167 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.00 % Allowed : 18.41 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.25 (0.41), residues: 418 helix: 1.22 (0.28), residues: 342 sheet: None (None), residues: 0 loop : -0.70 (0.67), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 143 HIS 0.002 0.001 HIS A 338 PHE 0.009 0.001 PHE A 310 TYR 0.015 0.001 TYR A 94 ARG 0.004 0.000 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.345 Fit side-chains REVERT: A 131 MET cc_start: 0.9037 (mtp) cc_final: 0.8684 (mtp) REVERT: A 143 TRP cc_start: 0.7567 (t60) cc_final: 0.7112 (t60) REVERT: A 297 TYR cc_start: 0.7128 (m-80) cc_final: 0.6641 (t80) REVERT: A 305 PHE cc_start: 0.7155 (m-80) cc_final: 0.6620 (m-80) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.7898 time to fit residues: 58.7273 Evaluate side-chains 62 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 21 optimal weight: 5.9990 chunk 32 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 20 optimal weight: 20.0000 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 HIS A 223 GLN A 307 ASN A 320 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.160961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.132042 restraints weight = 4305.073| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 2.43 r_work: 0.3499 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3371 Z= 0.223 Angle : 0.639 6.852 4590 Z= 0.332 Chirality : 0.042 0.242 543 Planarity : 0.005 0.062 555 Dihedral : 4.976 55.638 454 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 4.25 % Allowed : 15.30 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.68 (0.40), residues: 418 helix: 1.57 (0.27), residues: 352 sheet: None (None), residues: 0 loop : -1.22 (0.67), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 143 HIS 0.002 0.001 HIS A 338 PHE 0.014 0.002 PHE A 472 TYR 0.022 0.001 TYR A 94 ARG 0.003 0.001 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.322 Fit side-chains REVERT: A 305 PHE cc_start: 0.6836 (m-80) cc_final: 0.5995 (m-80) REVERT: A 370 ARG cc_start: 0.7539 (tpt90) cc_final: 0.7178 (mmt180) outliers start: 15 outliers final: 1 residues processed: 69 average time/residue: 0.7846 time to fit residues: 56.5049 Evaluate side-chains 54 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 53 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 10.0000 chunk 10 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 0 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN A 109 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.158144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.131439 restraints weight = 4223.249| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 2.25 r_work: 0.3448 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3371 Z= 0.208 Angle : 0.605 7.743 4590 Z= 0.314 Chirality : 0.041 0.232 543 Planarity : 0.005 0.041 555 Dihedral : 4.903 53.235 454 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.12 % Allowed : 16.71 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 (0.41), residues: 418 helix: 1.68 (0.27), residues: 355 sheet: None (None), residues: 0 loop : -1.10 (0.71), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 143 HIS 0.002 0.001 HIS A 338 PHE 0.017 0.002 PHE A 91 TYR 0.021 0.001 TYR A 94 ARG 0.002 0.000 ARG A 370 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.367 Fit side-chains REVERT: A 297 TYR cc_start: 0.6684 (m-80) cc_final: 0.6054 (t80) REVERT: A 305 PHE cc_start: 0.6946 (m-80) cc_final: 0.6362 (m-80) REVERT: A 370 ARG cc_start: 0.7350 (tpt90) cc_final: 0.7139 (mpt180) REVERT: A 429 LEU cc_start: 0.6303 (mt) cc_final: 0.6100 (mt) outliers start: 11 outliers final: 4 residues processed: 65 average time/residue: 0.6953 time to fit residues: 47.4809 Evaluate side-chains 52 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 402 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 26 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 32 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 34 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 13 optimal weight: 8.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.156682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.130458 restraints weight = 4288.882| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 2.24 r_work: 0.3464 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3371 Z= 0.260 Angle : 0.613 7.080 4590 Z= 0.318 Chirality : 0.042 0.225 543 Planarity : 0.005 0.051 555 Dihedral : 4.874 50.739 454 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 4.25 % Allowed : 17.28 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 (0.40), residues: 418 helix: 1.60 (0.27), residues: 354 sheet: None (None), residues: 0 loop : -0.82 (0.73), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 102 HIS 0.003 0.001 HIS A 338 PHE 0.020 0.002 PHE A 100 TYR 0.023 0.001 TYR A 94 ARG 0.001 0.000 ARG A 82 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 57 time to evaluate : 0.363 Fit side-chains REVERT: A 242 ASP cc_start: 0.7912 (t0) cc_final: 0.7575 (t0) REVERT: A 245 GLU cc_start: 0.7702 (mt-10) cc_final: 0.7304 (mp0) REVERT: A 274 GLU cc_start: 0.7104 (OUTLIER) cc_final: 0.6746 (tt0) REVERT: A 297 TYR cc_start: 0.6785 (m-80) cc_final: 0.6093 (t80) REVERT: A 305 PHE cc_start: 0.7111 (m-80) cc_final: 0.6595 (m-80) REVERT: A 369 ASP cc_start: 0.8617 (t70) cc_final: 0.8305 (t0) REVERT: A 437 ILE cc_start: 0.7013 (mm) cc_final: 0.6658 (mm) REVERT: A 486 PHE cc_start: 0.8439 (m-80) cc_final: 0.8213 (m-80) outliers start: 15 outliers final: 5 residues processed: 67 average time/residue: 0.7008 time to fit residues: 49.3040 Evaluate side-chains 60 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 402 TRP Chi-restraints excluded: chain A residue 484 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 21 optimal weight: 10.0000 chunk 39 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 chunk 31 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.158441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.131870 restraints weight = 4270.711| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.28 r_work: 0.3481 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3371 Z= 0.216 Angle : 0.587 7.585 4590 Z= 0.307 Chirality : 0.041 0.238 543 Planarity : 0.005 0.040 555 Dihedral : 4.881 52.224 454 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.68 % Allowed : 17.85 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.96 (0.41), residues: 418 helix: 1.69 (0.27), residues: 354 sheet: None (None), residues: 0 loop : -0.76 (0.72), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 102 HIS 0.003 0.001 HIS A 338 PHE 0.021 0.002 PHE A 100 TYR 0.022 0.001 TYR A 94 ARG 0.001 0.000 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.389 Fit side-chains REVERT: A 82 ARG cc_start: 0.6984 (OUTLIER) cc_final: 0.6496 (tpp80) REVERT: A 127 SER cc_start: 0.8741 (OUTLIER) cc_final: 0.8361 (m) REVERT: A 242 ASP cc_start: 0.7875 (t0) cc_final: 0.7439 (t0) REVERT: A 245 GLU cc_start: 0.7537 (mt-10) cc_final: 0.7191 (mp0) REVERT: A 297 TYR cc_start: 0.6785 (m-80) cc_final: 0.6086 (t80) REVERT: A 305 PHE cc_start: 0.7133 (m-80) cc_final: 0.6631 (m-80) REVERT: A 369 ASP cc_start: 0.8576 (t70) cc_final: 0.8344 (t0) REVERT: A 376 GLU cc_start: 0.7295 (mm-30) cc_final: 0.6567 (mp0) REVERT: A 437 ILE cc_start: 0.6953 (mm) cc_final: 0.6651 (mm) REVERT: A 486 PHE cc_start: 0.8439 (m-80) cc_final: 0.8205 (m-80) outliers start: 13 outliers final: 5 residues processed: 75 average time/residue: 0.9950 time to fit residues: 77.3058 Evaluate side-chains 57 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ARG Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 402 TRP Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 484 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 25 optimal weight: 0.0050 chunk 32 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 chunk 7 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.161299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.133613 restraints weight = 4325.104| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 2.43 r_work: 0.3508 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3371 Z= 0.203 Angle : 0.588 6.968 4590 Z= 0.307 Chirality : 0.041 0.235 543 Planarity : 0.005 0.047 555 Dihedral : 4.919 54.834 454 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.12 % Allowed : 20.68 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 2.15 (0.41), residues: 418 helix: 1.79 (0.27), residues: 353 sheet: None (None), residues: 0 loop : -0.51 (0.75), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 102 HIS 0.003 0.001 HIS A 338 PHE 0.014 0.002 PHE A 472 TYR 0.021 0.001 TYR A 94 ARG 0.002 0.000 ARG A 303 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.339 Fit side-chains REVERT: A 82 ARG cc_start: 0.6951 (OUTLIER) cc_final: 0.6478 (tpp80) REVERT: A 242 ASP cc_start: 0.7945 (t0) cc_final: 0.7594 (t0) REVERT: A 245 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7271 (mp0) REVERT: A 297 TYR cc_start: 0.6773 (m-80) cc_final: 0.6046 (t80) REVERT: A 305 PHE cc_start: 0.7090 (m-80) cc_final: 0.6565 (m-80) REVERT: A 369 ASP cc_start: 0.8463 (t70) cc_final: 0.8228 (t0) REVERT: A 376 GLU cc_start: 0.7194 (mm-30) cc_final: 0.6479 (mp0) REVERT: A 402 TRP cc_start: 0.5536 (OUTLIER) cc_final: 0.5079 (p-90) REVERT: A 437 ILE cc_start: 0.6859 (mm) cc_final: 0.6585 (mm) REVERT: A 486 PHE cc_start: 0.8408 (m-80) cc_final: 0.8098 (m-80) outliers start: 11 outliers final: 5 residues processed: 68 average time/residue: 0.8722 time to fit residues: 61.6678 Evaluate side-chains 57 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ARG Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 402 TRP Chi-restraints excluded: chain A residue 428 GLU Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 484 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 27 optimal weight: 2.9990 chunk 13 optimal weight: 0.1980 chunk 33 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3923 r_free = 0.3923 target = 0.161244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.133560 restraints weight = 4246.508| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.40 r_work: 0.3522 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3371 Z= 0.199 Angle : 0.582 7.484 4590 Z= 0.303 Chirality : 0.040 0.234 543 Planarity : 0.005 0.037 555 Dihedral : 4.910 54.894 454 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.83 % Allowed : 21.81 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 2.20 (0.41), residues: 418 helix: 1.83 (0.27), residues: 353 sheet: None (None), residues: 0 loop : -0.49 (0.76), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 102 HIS 0.003 0.001 HIS A 338 PHE 0.014 0.001 PHE A 472 TYR 0.022 0.001 TYR A 94 ARG 0.005 0.000 ARG A 303 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.355 Fit side-chains REVERT: A 82 ARG cc_start: 0.6651 (OUTLIER) cc_final: 0.6219 (tpp80) REVERT: A 242 ASP cc_start: 0.7904 (t0) cc_final: 0.7430 (t0) REVERT: A 245 GLU cc_start: 0.7525 (mt-10) cc_final: 0.7208 (mp0) REVERT: A 297 TYR cc_start: 0.6807 (m-80) cc_final: 0.6025 (t80) REVERT: A 305 PHE cc_start: 0.7108 (m-80) cc_final: 0.6570 (m-80) REVERT: A 369 ASP cc_start: 0.8471 (t70) cc_final: 0.8222 (t0) REVERT: A 376 GLU cc_start: 0.7189 (mm-30) cc_final: 0.6448 (mp0) REVERT: A 402 TRP cc_start: 0.5508 (OUTLIER) cc_final: 0.5059 (p-90) REVERT: A 437 ILE cc_start: 0.6860 (mm) cc_final: 0.6610 (mm) REVERT: A 486 PHE cc_start: 0.8372 (m-80) cc_final: 0.8094 (m-80) outliers start: 10 outliers final: 2 residues processed: 67 average time/residue: 0.8502 time to fit residues: 59.2382 Evaluate side-chains 54 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ARG Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 402 TRP Chi-restraints excluded: chain A residue 484 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 13 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 20 optimal weight: 40.0000 chunk 33 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3938 r_free = 0.3938 target = 0.161636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.134714 restraints weight = 4214.630| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 2.32 r_work: 0.3532 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3371 Z= 0.208 Angle : 0.587 7.281 4590 Z= 0.306 Chirality : 0.040 0.237 543 Planarity : 0.005 0.045 555 Dihedral : 4.946 53.914 454 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.98 % Allowed : 22.10 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 2.17 (0.40), residues: 418 helix: 1.81 (0.27), residues: 353 sheet: None (None), residues: 0 loop : -0.50 (0.75), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 102 HIS 0.003 0.001 HIS A 338 PHE 0.015 0.001 PHE A 472 TYR 0.022 0.001 TYR A 94 ARG 0.005 0.000 ARG A 303 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.330 Fit side-chains REVERT: A 82 ARG cc_start: 0.6615 (OUTLIER) cc_final: 0.6233 (tpp80) REVERT: A 242 ASP cc_start: 0.7774 (t0) cc_final: 0.7443 (t0) REVERT: A 245 GLU cc_start: 0.7507 (mt-10) cc_final: 0.7200 (mp0) REVERT: A 297 TYR cc_start: 0.6797 (m-80) cc_final: 0.5996 (t80) REVERT: A 369 ASP cc_start: 0.8488 (t70) cc_final: 0.8234 (t0) REVERT: A 376 GLU cc_start: 0.7244 (mm-30) cc_final: 0.6531 (mp0) REVERT: A 437 ILE cc_start: 0.6937 (mm) cc_final: 0.6672 (mm) REVERT: A 486 PHE cc_start: 0.8407 (m-80) cc_final: 0.8095 (m-80) outliers start: 7 outliers final: 3 residues processed: 61 average time/residue: 0.7894 time to fit residues: 50.3239 Evaluate side-chains 54 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ARG Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 484 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 5.9990 chunk 15 optimal weight: 0.2980 chunk 13 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 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 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.162652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.135349 restraints weight = 4262.244| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.35 r_work: 0.3526 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3371 Z= 0.187 Angle : 0.580 7.872 4590 Z= 0.304 Chirality : 0.040 0.238 543 Planarity : 0.005 0.040 555 Dihedral : 4.953 54.082 454 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 2.27 % Allowed : 22.95 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 2.22 (0.40), residues: 418 helix: 1.86 (0.27), residues: 354 sheet: None (None), residues: 0 loop : -0.63 (0.73), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 102 HIS 0.006 0.001 HIS A 338 PHE 0.014 0.001 PHE A 472 TYR 0.025 0.001 TYR A 392 ARG 0.005 0.000 ARG A 303 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.278 Fit side-chains REVERT: A 82 ARG cc_start: 0.6605 (OUTLIER) cc_final: 0.6225 (tpp80) REVERT: A 242 ASP cc_start: 0.7769 (t0) cc_final: 0.7423 (t0) REVERT: A 245 GLU cc_start: 0.7391 (mt-10) cc_final: 0.7098 (mp0) REVERT: A 297 TYR cc_start: 0.6833 (m-80) cc_final: 0.6060 (t80) REVERT: A 305 PHE cc_start: 0.7070 (m-80) cc_final: 0.6521 (m-80) REVERT: A 369 ASP cc_start: 0.8441 (t70) cc_final: 0.8223 (t0) REVERT: A 376 GLU cc_start: 0.7270 (mm-30) cc_final: 0.6564 (mp0) REVERT: A 437 ILE cc_start: 0.6882 (mm) cc_final: 0.6639 (mm) REVERT: A 486 PHE cc_start: 0.8454 (m-80) cc_final: 0.8150 (m-80) outliers start: 8 outliers final: 2 residues processed: 61 average time/residue: 0.7897 time to fit residues: 50.2885 Evaluate side-chains 58 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 55 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ARG Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 484 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 36 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 5 optimal weight: 0.2980 chunk 20 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 40 optimal weight: 5.9990 chunk 14 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.162151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.135021 restraints weight = 4205.665| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 2.31 r_work: 0.3538 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3371 Z= 0.202 Angle : 0.617 8.798 4590 Z= 0.320 Chirality : 0.041 0.237 543 Planarity : 0.005 0.044 555 Dihedral : 4.917 52.840 454 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.98 % Allowed : 24.36 % Favored : 73.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 2.24 (0.40), residues: 418 helix: 1.85 (0.27), residues: 353 sheet: None (None), residues: 0 loop : -0.44 (0.76), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 102 HIS 0.004 0.001 HIS A 338 PHE 0.014 0.002 PHE A 472 TYR 0.023 0.001 TYR A 94 ARG 0.004 0.000 ARG A 303 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.379 Fit side-chains REVERT: A 82 ARG cc_start: 0.6625 (OUTLIER) cc_final: 0.6261 (tpp80) REVERT: A 242 ASP cc_start: 0.7758 (t0) cc_final: 0.7400 (t0) REVERT: A 245 GLU cc_start: 0.7480 (mt-10) cc_final: 0.7212 (mp0) REVERT: A 297 TYR cc_start: 0.6816 (m-80) cc_final: 0.6145 (t80) REVERT: A 305 PHE cc_start: 0.7095 (m-80) cc_final: 0.6537 (m-80) REVERT: A 376 GLU cc_start: 0.7275 (mm-30) cc_final: 0.6588 (mp0) REVERT: A 486 PHE cc_start: 0.8457 (m-80) cc_final: 0.8160 (m-80) outliers start: 7 outliers final: 3 residues processed: 64 average time/residue: 0.8222 time to fit residues: 54.9572 Evaluate side-chains 58 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 54 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ARG Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 484 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 38 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 12 optimal weight: 0.3980 chunk 40 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.162576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.135482 restraints weight = 4203.040| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 2.31 r_work: 0.3539 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.3781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3371 Z= 0.212 Angle : 0.626 8.759 4590 Z= 0.327 Chirality : 0.041 0.236 543 Planarity : 0.005 0.042 555 Dihedral : 4.929 52.285 454 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.70 % Allowed : 24.65 % Favored : 73.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 2.33 (0.40), residues: 418 helix: 1.93 (0.27), residues: 350 sheet: None (None), residues: 0 loop : -0.44 (0.76), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 102 HIS 0.004 0.001 HIS A 338 PHE 0.014 0.001 PHE A 472 TYR 0.023 0.001 TYR A 392 ARG 0.004 0.000 ARG A 303 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2389.90 seconds wall clock time: 42 minutes 58.79 seconds (2578.79 seconds total)