Starting phenix.real_space_refine on Tue Aug 4 16:35:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vc8_64948/08_2026/9vc8_64948.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vc8_64948/08_2026/9vc8_64948.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vc8_64948/08_2026/9vc8_64948.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vc8_64948/08_2026/9vc8_64948.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vc8_64948/08_2026/9vc8_64948.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vc8_64948/08_2026/9vc8_64948.map" } resolution = 4.04 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.029 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 28 5.16 5 C 3074 2.51 5 N 821 2.21 5 O 873 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4796 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 599, 4796 Classifications: {'peptide': 599} Link IDs: {'PTRANS': 32, 'TRANS': 566} Time building chain proxies: 1.34, per 1000 atoms: 0.28 Number of scatterers: 4796 At special positions: 0 Unit cell: (83.83, 74.7, 107.9, 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 28 16.00 O 873 8.00 N 821 7.00 C 3074 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: 0.48 Conformation dependent library (CDL) restraints added in 211.5 milliseconds 1194 Ramachandran restraints generated. 597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1142 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 3 sheets defined 59.9% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 90 through 103 Processing helix chain 'A' and resid 103 through 113 removed outlier: 3.675A pdb=" N GLN A 107 " --> pdb=" O ARG A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 134 removed outlier: 3.733A pdb=" N SER A 134 " --> pdb=" O TYR A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 151 Processing helix chain 'A' and resid 154 through 157 Processing helix chain 'A' and resid 158 through 170 Processing helix chain 'A' and resid 171 through 183 removed outlier: 3.916A pdb=" N CYS A 175 " --> pdb=" O PRO A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 191 Processing helix chain 'A' and resid 192 through 198 removed outlier: 4.193A pdb=" N MET A 198 " --> pdb=" O ASP A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 224 removed outlier: 3.526A pdb=" N HIS A 216 " --> pdb=" O GLY A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 248 Processing helix chain 'A' and resid 292 through 298 removed outlier: 3.771A pdb=" N ARG A 297 " --> pdb=" O GLN A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 312 removed outlier: 3.887A pdb=" N TRP A 305 " --> pdb=" O ARG A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 324 No H-bonds generated for 'chain 'A' and resid 322 through 324' Processing helix chain 'A' and resid 325 through 336 Processing helix chain 'A' and resid 360 through 364 Processing helix chain 'A' and resid 374 through 389 Processing helix chain 'A' and resid 400 through 413 Processing helix chain 'A' and resid 425 through 429 Processing helix chain 'A' and resid 460 through 470 Processing helix chain 'A' and resid 487 through 500 removed outlier: 3.724A pdb=" N ARG A 500 " --> pdb=" O GLU A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 524 Processing helix chain 'A' and resid 528 through 540 Processing helix chain 'A' and resid 551 through 562 Processing helix chain 'A' and resid 567 through 576 Processing helix chain 'A' and resid 583 through 600 removed outlier: 3.900A pdb=" N CYS A 587 " --> pdb=" O GLN A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 613 removed outlier: 3.547A pdb=" N LEU A 608 " --> pdb=" O THR A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 643 Processing helix chain 'A' and resid 651 through 672 removed outlier: 3.617A pdb=" N ILE A 655 " --> pdb=" O ASP A 651 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN A 672 " --> pdb=" O ASP A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 682 removed outlier: 3.526A pdb=" N LEU A 676 " --> pdb=" O ASN A 672 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.154A pdb=" N ASP A 252 " --> pdb=" O SER A 273 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N GLU A 286 " --> pdb=" O GLU A 316 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N HIS A 318 " --> pdb=" O GLU A 286 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N ALA A 288 " --> pdb=" O HIS A 318 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N CYS A 320 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N ILE A 290 " --> pdb=" O CYS A 320 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY A 321 " --> pdb=" O HIS A 205 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 392 through 395 removed outlier: 6.099A pdb=" N ILE A 438 " --> pdb=" O THR A 484 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 444 through 448 260 hydrogen bonds defined for protein. 744 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: 0.78 Time building geometry restraints manager: 0.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1566 1.34 - 1.46: 779 1.46 - 1.58: 2519 1.58 - 1.69: 0 1.69 - 1.81: 42 Bond restraints: 4906 Sorted by residual: bond pdb=" C PRO A 188 " pdb=" N PRO A 189 " ideal model delta sigma weight residual 1.335 1.349 -0.014 1.19e-02 7.06e+03 1.47e+00 bond pdb=" N GLU A 601 " pdb=" CA GLU A 601 " ideal model delta sigma weight residual 1.453 1.465 -0.012 1.18e-02 7.18e+03 1.00e+00 bond pdb=" N LEU A 524 " pdb=" CA LEU A 524 " ideal model delta sigma weight residual 1.463 1.453 0.010 1.08e-02 8.57e+03 8.79e-01 bond pdb=" C TRP A 614 " pdb=" N PRO A 615 " ideal model delta sigma weight residual 1.334 1.355 -0.021 2.34e-02 1.83e+03 8.20e-01 bond pdb=" CB ILE A 439 " pdb=" CG2 ILE A 439 " ideal model delta sigma weight residual 1.521 1.494 0.027 3.30e-02 9.18e+02 6.51e-01 ... (remaining 4901 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 6411 1.40 - 2.80: 192 2.80 - 4.20: 34 4.20 - 5.60: 5 5.60 - 7.01: 2 Bond angle restraints: 6644 Sorted by residual: angle pdb=" N ARG A 477 " pdb=" CA ARG A 477 " pdb=" C ARG A 477 " ideal model delta sigma weight residual 112.93 108.23 4.70 1.33e+00 5.65e-01 1.25e+01 angle pdb=" N ILE A 427 " pdb=" CA ILE A 427 " pdb=" C ILE A 427 " ideal model delta sigma weight residual 113.00 109.05 3.95 1.30e+00 5.92e-01 9.22e+00 angle pdb=" CA MET A 295 " pdb=" CB MET A 295 " pdb=" CG MET A 295 " ideal model delta sigma weight residual 114.10 119.95 -5.85 2.00e+00 2.50e-01 8.56e+00 angle pdb=" N ARG A 180 " pdb=" CA ARG A 180 " pdb=" C ARG A 180 " ideal model delta sigma weight residual 111.28 108.32 2.96 1.09e+00 8.42e-01 7.38e+00 angle pdb=" N THR A 485 " pdb=" CA THR A 485 " pdb=" C THR A 485 " ideal model delta sigma weight residual 108.45 111.76 -3.31 1.26e+00 6.30e-01 6.92e+00 ... (remaining 6639 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.04: 2620 14.04 - 28.08: 243 28.08 - 42.12: 91 42.12 - 56.16: 17 56.16 - 70.21: 16 Dihedral angle restraints: 2987 sinusoidal: 1227 harmonic: 1760 Sorted by residual: dihedral pdb=" CA ASP A 298 " pdb=" CB ASP A 298 " pdb=" CG ASP A 298 " pdb=" OD1 ASP A 298 " ideal model delta sinusoidal sigma weight residual -30.00 -87.56 57.56 1 2.00e+01 2.50e-03 1.11e+01 dihedral pdb=" CA MET A 486 " pdb=" C MET A 486 " pdb=" N ASN A 487 " pdb=" CA ASN A 487 " ideal model delta harmonic sigma weight residual 180.00 -164.32 -15.68 0 5.00e+00 4.00e-02 9.83e+00 dihedral pdb=" CA TYR A 396 " pdb=" C TYR A 396 " pdb=" N GLY A 397 " pdb=" CA GLY A 397 " ideal model delta harmonic sigma weight residual -180.00 -164.84 -15.16 0 5.00e+00 4.00e-02 9.19e+00 ... (remaining 2984 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 492 0.030 - 0.060: 162 0.060 - 0.089: 49 0.089 - 0.119: 35 0.119 - 0.149: 3 Chirality restraints: 741 Sorted by residual: chirality pdb=" CA ILE A 439 " pdb=" N ILE A 439 " pdb=" C ILE A 439 " pdb=" CB ILE A 439 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.55e-01 chirality pdb=" CA VAL A 340 " pdb=" N VAL A 340 " pdb=" C VAL A 340 " pdb=" CB VAL A 340 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.99e-01 chirality pdb=" CA ILE A 395 " pdb=" N ILE A 395 " pdb=" C ILE A 395 " pdb=" CB ILE A 395 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.65e-01 ... (remaining 738 not shown) Planarity restraints: 855 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 188 " 0.026 5.00e-02 4.00e+02 3.88e-02 2.41e+00 pdb=" N PRO A 189 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 189 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 189 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 640 " -0.009 2.00e-02 2.50e+03 9.21e-03 2.12e+00 pdb=" CG TRP A 640 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP A 640 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP A 640 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 640 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 640 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 640 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 640 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 640 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 640 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 100 " -0.011 2.00e-02 2.50e+03 1.06e-02 1.95e+00 pdb=" CG PHE A 100 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE A 100 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE A 100 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE A 100 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 100 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 100 " -0.000 2.00e-02 2.50e+03 ... (remaining 852 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 873 2.77 - 3.30: 5159 3.30 - 3.83: 8285 3.83 - 4.37: 9901 4.37 - 4.90: 15577 Nonbonded interactions: 39795 Sorted by model distance: nonbonded pdb=" O ASN A 363 " pdb=" ND2 ASN A 363 " model vdw 2.233 3.120 nonbonded pdb=" OG1 THR A 209 " pdb=" NE2 GLN A 466 " model vdw 2.298 3.120 nonbonded pdb=" O PRO A 189 " pdb=" NH1 ARG A 196 " model vdw 2.300 3.120 nonbonded pdb=" O ARG A 595 " pdb=" OG SER A 598 " model vdw 2.310 3.040 nonbonded pdb=" O LEU A 431 " pdb=" NH1 ARG A 470 " model vdw 2.322 3.120 ... (remaining 39790 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.610 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 6.640 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 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 0.036 4906 Z= 0.140 Angle : 0.602 7.006 6644 Z= 0.352 Chirality : 0.038 0.149 741 Planarity : 0.004 0.039 855 Dihedral : 13.804 70.206 1845 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 0.19 % Allowed : 0.00 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.36), residues: 597 helix: 1.47 (0.29), residues: 330 sheet: -0.61 (0.67), residues: 62 loop : -0.93 (0.47), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 644 TYR 0.010 0.001 TYR A 572 PHE 0.025 0.002 PHE A 100 TRP 0.024 0.001 TRP A 640 HIS 0.002 0.001 HIS A 632 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.14 ( 4906) covalent geometry : angle 0.60170 / 0.35 ( 6644) hydrogen bonds : bond 0.17134 / 11.12 ( 260) hydrogen bonds : angle 6.02604 / 4.33 ( 744) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1194 Ramachandran restraints generated. 597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1194 Ramachandran restraints generated. 597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 81 time to evaluate : 0.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 LEU cc_start: 0.8699 (mt) cc_final: 0.8485 (mm) REVERT: A 291 ASP cc_start: 0.8004 (t0) cc_final: 0.7747 (t0) REVERT: A 416 ASP cc_start: 0.8720 (t0) cc_final: 0.8489 (t0) outliers start: 1 outliers final: 1 residues processed: 82 average time/residue: 0.0785 time to fit residues: 8.3962 Evaluate side-chains 64 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 63 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 54 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 26 optimal weight: 0.3980 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 chunk 58 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 245 ASN A 466 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.124474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.093707 restraints weight = 17979.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.096102 restraints weight = 12317.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.097776 restraints weight = 9328.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.098658 restraints weight = 7608.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.099735 restraints weight = 6676.895| |-----------------------------------------------------------------------------| r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.1029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4906 Z= 0.157 Angle : 0.552 5.367 6644 Z= 0.293 Chirality : 0.039 0.128 741 Planarity : 0.005 0.036 855 Dihedral : 4.153 18.642 651 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.36), residues: 597 helix: 1.63 (0.29), residues: 326 sheet: -0.95 (0.64), residues: 61 loop : -0.75 (0.47), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 610 TYR 0.016 0.001 TYR A 379 PHE 0.025 0.002 PHE A 100 TRP 0.008 0.001 TRP A 640 HIS 0.005 0.001 HIS A 632 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.16 ( 4906) covalent geometry : angle 0.55163 / 0.29 ( 6644) hydrogen bonds : bond 0.04321 / 2.78 ( 260) hydrogen bonds : angle 5.07441 / 3.71 ( 744) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1194 Ramachandran restraints generated. 597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1194 Ramachandran restraints generated. 597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 PHE cc_start: 0.9179 (m-80) cc_final: 0.8903 (m-10) REVERT: A 179 LEU cc_start: 0.8744 (mt) cc_final: 0.8540 (mt) REVERT: A 291 ASP cc_start: 0.8119 (t0) cc_final: 0.7909 (t70) REVERT: A 295 MET cc_start: 0.8998 (tpp) cc_final: 0.8646 (tpp) REVERT: A 348 LEU cc_start: 0.8321 (mm) cc_final: 0.8077 (mm) REVERT: A 416 ASP cc_start: 0.8743 (t0) cc_final: 0.8496 (t0) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.0747 time to fit residues: 8.0676 Evaluate side-chains 68 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 43 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 57 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 13 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 chunk 46 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 38 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 210 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.125810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.095331 restraints weight = 18174.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.097711 restraints weight = 12120.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.099411 restraints weight = 9115.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.100486 restraints weight = 7380.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.101401 restraints weight = 6390.234| |-----------------------------------------------------------------------------| r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4906 Z= 0.122 Angle : 0.503 5.143 6644 Z= 0.266 Chirality : 0.038 0.141 741 Planarity : 0.004 0.039 855 Dihedral : 4.123 17.693 651 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.36), residues: 597 helix: 1.67 (0.29), residues: 326 sheet: -1.04 (0.63), residues: 59 loop : -0.84 (0.46), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 610 TYR 0.019 0.001 TYR A 379 PHE 0.029 0.002 PHE A 593 TRP 0.010 0.001 TRP A 640 HIS 0.003 0.001 HIS A 632 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 ( 4906) covalent geometry : angle 0.50260 / 0.27 ( 6644) hydrogen bonds : bond 0.03712 / 2.41 ( 260) hydrogen bonds : angle 4.71579 / 3.43 ( 744) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1194 Ramachandran restraints generated. 597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1194 Ramachandran restraints generated. 597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 LEU cc_start: 0.8667 (mt) cc_final: 0.8412 (mp) REVERT: A 291 ASP cc_start: 0.8162 (t0) cc_final: 0.7945 (t70) REVERT: A 295 MET cc_start: 0.8952 (tpp) cc_final: 0.8531 (tpp) REVERT: A 301 ARG cc_start: 0.8137 (mtm180) cc_final: 0.7779 (mtm-85) REVERT: A 303 TRP cc_start: 0.7635 (p-90) cc_final: 0.7248 (p-90) REVERT: A 348 LEU cc_start: 0.8405 (mm) cc_final: 0.8164 (mm) REVERT: A 416 ASP cc_start: 0.8688 (t0) cc_final: 0.8465 (t0) REVERT: A 560 LEU cc_start: 0.9034 (mm) cc_final: 0.8617 (mm) REVERT: A 644 ARG cc_start: 0.8142 (mmt180) cc_final: 0.7706 (mmt90) REVERT: A 648 MET cc_start: 0.7101 (mmm) cc_final: 0.6890 (mmt) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.0727 time to fit residues: 7.9671 Evaluate side-chains 69 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 6 optimal weight: 0.0000 chunk 36 optimal weight: 9.9990 chunk 23 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 52 optimal weight: 0.0980 chunk 33 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 20 optimal weight: 0.4980 chunk 38 optimal weight: 10.0000 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.127304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.096648 restraints weight = 17824.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.099078 restraints weight = 12081.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.100827 restraints weight = 9083.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.101798 restraints weight = 7312.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.102636 restraints weight = 6368.926| |-----------------------------------------------------------------------------| r_work (final): 0.3955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 4906 Z= 0.102 Angle : 0.483 5.015 6644 Z= 0.252 Chirality : 0.039 0.200 741 Planarity : 0.004 0.040 855 Dihedral : 3.998 17.689 651 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.36), residues: 597 helix: 1.76 (0.29), residues: 327 sheet: -0.69 (0.58), residues: 70 loop : -0.94 (0.48), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 388 TYR 0.021 0.001 TYR A 379 PHE 0.025 0.001 PHE A 593 TRP 0.011 0.001 TRP A 640 HIS 0.003 0.001 HIS A 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 ( 4906) covalent geometry : angle 0.48346 / 0.25 ( 6644) hydrogen bonds : bond 0.03274 / 2.13 ( 260) hydrogen bonds : angle 4.42234 / 3.20 ( 744) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1194 Ramachandran restraints generated. 597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1194 Ramachandran restraints generated. 597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 LEU cc_start: 0.8667 (mt) cc_final: 0.8419 (mp) REVERT: A 291 ASP cc_start: 0.8206 (t0) cc_final: 0.8001 (t70) REVERT: A 295 MET cc_start: 0.8922 (tpp) cc_final: 0.8461 (tpp) REVERT: A 301 ARG cc_start: 0.8094 (mtm180) cc_final: 0.7755 (mtm-85) REVERT: A 303 TRP cc_start: 0.7581 (p-90) cc_final: 0.7180 (p-90) REVERT: A 416 ASP cc_start: 0.8688 (t0) cc_final: 0.8439 (t0) REVERT: A 465 LEU cc_start: 0.8701 (tp) cc_final: 0.8467 (mt) REVERT: A 519 MET cc_start: 0.8324 (tpt) cc_final: 0.7972 (mtt) REVERT: A 560 LEU cc_start: 0.9016 (mm) cc_final: 0.8595 (mm) REVERT: A 644 ARG cc_start: 0.8070 (mmt180) cc_final: 0.7714 (mmt90) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.0718 time to fit residues: 7.7186 Evaluate side-chains 70 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 17 optimal weight: 8.9990 chunk 11 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 30 optimal weight: 0.0370 chunk 2 optimal weight: 9.9990 chunk 41 optimal weight: 0.0980 chunk 29 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 5 optimal weight: 8.9990 chunk 40 optimal weight: 0.9980 overall best weight: 1.2260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 363 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.124776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.094271 restraints weight = 18506.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.096592 restraints weight = 12561.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.098151 restraints weight = 9510.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.099382 restraints weight = 7793.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.100149 restraints weight = 6653.563| |-----------------------------------------------------------------------------| r_work (final): 0.3918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4906 Z= 0.131 Angle : 0.518 5.882 6644 Z= 0.270 Chirality : 0.039 0.142 741 Planarity : 0.004 0.036 855 Dihedral : 4.057 18.061 651 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 0.19 % Allowed : 1.13 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.36), residues: 597 helix: 1.74 (0.29), residues: 326 sheet: -0.76 (0.57), residues: 71 loop : -0.74 (0.49), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 164 TYR 0.018 0.001 TYR A 379 PHE 0.039 0.002 PHE A 100 TRP 0.016 0.002 TRP A 640 HIS 0.004 0.001 HIS A 632 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 ( 4906) covalent geometry : angle 0.51808 / 0.27 ( 6644) hydrogen bonds : bond 0.03377 / 2.20 ( 260) hydrogen bonds : angle 4.41440 / 3.21 ( 744) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1194 Ramachandran restraints generated. 597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1194 Ramachandran restraints generated. 597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 76 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 LEU cc_start: 0.8684 (mt) cc_final: 0.8431 (mp) REVERT: A 291 ASP cc_start: 0.8104 (t0) cc_final: 0.7902 (t70) REVERT: A 295 MET cc_start: 0.8909 (tpp) cc_final: 0.8405 (tpp) REVERT: A 301 ARG cc_start: 0.8126 (mtm180) cc_final: 0.7786 (mtm-85) REVERT: A 303 TRP cc_start: 0.7658 (p-90) cc_final: 0.7286 (p-90) REVERT: A 348 LEU cc_start: 0.9037 (tp) cc_final: 0.8805 (pp) REVERT: A 416 ASP cc_start: 0.8771 (t0) cc_final: 0.8462 (t0) outliers start: 1 outliers final: 0 residues processed: 77 average time/residue: 0.0712 time to fit residues: 7.3261 Evaluate side-chains 66 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 54 optimal weight: 6.9990 chunk 5 optimal weight: 20.0000 chunk 47 optimal weight: 0.2980 chunk 12 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 10 optimal weight: 0.4980 chunk 23 optimal weight: 0.9990 chunk 7 optimal weight: 10.0000 chunk 31 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.124244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.093360 restraints weight = 19024.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.095745 restraints weight = 12983.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.097227 restraints weight = 9823.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.098499 restraints weight = 8082.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.099431 restraints weight = 6930.836| |-----------------------------------------------------------------------------| r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4906 Z= 0.129 Angle : 0.515 6.037 6644 Z= 0.268 Chirality : 0.040 0.280 741 Planarity : 0.004 0.035 855 Dihedral : 4.069 17.735 651 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.36), residues: 597 helix: 1.88 (0.29), residues: 320 sheet: -0.83 (0.56), residues: 71 loop : -0.75 (0.48), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 128 TYR 0.018 0.001 TYR A 379 PHE 0.024 0.001 PHE A 593 TRP 0.013 0.002 TRP A 640 HIS 0.004 0.001 HIS A 632 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 ( 4906) covalent geometry : angle 0.51473 / 0.27 ( 6644) hydrogen bonds : bond 0.03331 / 2.17 ( 260) hydrogen bonds : angle 4.39279 / 3.19 ( 744) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1194 Ramachandran restraints generated. 597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1194 Ramachandran restraints generated. 597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 LEU cc_start: 0.8677 (mt) cc_final: 0.8421 (mp) REVERT: A 291 ASP cc_start: 0.8127 (t0) cc_final: 0.7915 (t70) REVERT: A 295 MET cc_start: 0.8891 (tpp) cc_final: 0.8382 (tpp) REVERT: A 301 ARG cc_start: 0.8153 (mtm180) cc_final: 0.7833 (mtm-85) REVERT: A 303 TRP cc_start: 0.7613 (p-90) cc_final: 0.7255 (p-90) REVERT: A 348 LEU cc_start: 0.9058 (tp) cc_final: 0.8837 (pp) REVERT: A 416 ASP cc_start: 0.8747 (t0) cc_final: 0.8486 (t0) REVERT: A 519 MET cc_start: 0.8355 (tpt) cc_final: 0.7978 (mtt) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.0721 time to fit residues: 7.2314 Evaluate side-chains 65 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 39 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 6 optimal weight: 0.0670 chunk 46 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 20 optimal weight: 0.0370 chunk 8 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.126326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.095497 restraints weight = 18465.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.097905 restraints weight = 12487.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.099441 restraints weight = 9377.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.100738 restraints weight = 7673.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.101642 restraints weight = 6512.679| |-----------------------------------------------------------------------------| r_work (final): 0.3931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 4906 Z= 0.103 Angle : 0.512 6.506 6644 Z= 0.262 Chirality : 0.038 0.139 741 Planarity : 0.004 0.037 855 Dihedral : 3.988 17.610 651 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.36), residues: 597 helix: 1.73 (0.29), residues: 329 sheet: -0.67 (0.56), residues: 70 loop : -1.04 (0.47), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 196 TYR 0.020 0.001 TYR A 379 PHE 0.042 0.002 PHE A 100 TRP 0.014 0.001 TRP A 640 HIS 0.002 0.001 HIS A 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 ( 4906) covalent geometry : angle 0.51208 / 0.26 ( 6644) hydrogen bonds : bond 0.03060 / 2.00 ( 260) hydrogen bonds : angle 4.21748 / 3.06 ( 744) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1194 Ramachandran restraints generated. 597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1194 Ramachandran restraints generated. 597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 LEU cc_start: 0.8751 (mt) cc_final: 0.8498 (mt) REVERT: A 185 LEU cc_start: 0.8684 (mt) cc_final: 0.8409 (mp) REVERT: A 295 MET cc_start: 0.8887 (tpp) cc_final: 0.8393 (tpp) REVERT: A 301 ARG cc_start: 0.8132 (mtm180) cc_final: 0.7821 (mtm-85) REVERT: A 303 TRP cc_start: 0.7541 (p-90) cc_final: 0.7191 (p-90) REVERT: A 348 LEU cc_start: 0.9049 (tp) cc_final: 0.8844 (pp) REVERT: A 404 LYS cc_start: 0.8454 (tttt) cc_final: 0.8222 (tttm) REVERT: A 416 ASP cc_start: 0.8749 (t0) cc_final: 0.8505 (t0) REVERT: A 465 LEU cc_start: 0.8712 (tp) cc_final: 0.8502 (mt) REVERT: A 486 MET cc_start: 0.8394 (mmp) cc_final: 0.7210 (ttt) REVERT: A 560 LEU cc_start: 0.9017 (mm) cc_final: 0.8597 (mm) REVERT: A 644 ARG cc_start: 0.8252 (mmt180) cc_final: 0.7970 (mmt-90) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.0735 time to fit residues: 8.1042 Evaluate side-chains 74 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 41 optimal weight: 4.9990 chunk 0 optimal weight: 30.0000 chunk 7 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 25 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 8.9990 chunk 31 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 107 GLN A 121 HIS A 488 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.121267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.091701 restraints weight = 18281.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.093897 restraints weight = 12336.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.095472 restraints weight = 9334.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.096462 restraints weight = 7565.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.097410 restraints weight = 6559.404| |-----------------------------------------------------------------------------| r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4906 Z= 0.183 Angle : 0.601 7.775 6644 Z= 0.311 Chirality : 0.040 0.141 741 Planarity : 0.005 0.032 855 Dihedral : 4.305 19.135 651 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.35), residues: 597 helix: 1.63 (0.29), residues: 322 sheet: -1.01 (0.54), residues: 71 loop : -0.84 (0.47), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 610 TYR 0.036 0.002 TYR A 379 PHE 0.016 0.002 PHE A 593 TRP 0.013 0.002 TRP A 614 HIS 0.007 0.001 HIS A 632 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.18 ( 4906) covalent geometry : angle 0.60063 / 0.31 ( 6644) hydrogen bonds : bond 0.03611 / 2.40 ( 260) hydrogen bonds : angle 4.62249 / 3.38 ( 744) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1194 Ramachandran restraints generated. 597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1194 Ramachandran restraints generated. 597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 CYS cc_start: 0.7117 (m) cc_final: 0.6895 (m) REVERT: A 295 MET cc_start: 0.8907 (tpp) cc_final: 0.8366 (tpp) REVERT: A 303 TRP cc_start: 0.7707 (p-90) cc_final: 0.7371 (p-90) REVERT: A 519 MET cc_start: 0.8439 (tpt) cc_final: 0.8098 (mtt) REVERT: A 560 LEU cc_start: 0.9030 (mm) cc_final: 0.8650 (mm) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.0656 time to fit residues: 6.9241 Evaluate side-chains 69 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 34 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 11 optimal weight: 9.9990 chunk 47 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 22 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 146 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.119642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.090126 restraints weight = 18925.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.092351 restraints weight = 12914.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.093889 restraints weight = 9768.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.094846 restraints weight = 7932.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.095750 restraints weight = 6912.865| |-----------------------------------------------------------------------------| r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 4906 Z= 0.223 Angle : 0.671 9.172 6644 Z= 0.347 Chirality : 0.043 0.353 741 Planarity : 0.005 0.031 855 Dihedral : 4.584 18.807 651 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 16.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.35), residues: 597 helix: 1.37 (0.28), residues: 323 sheet: -1.09 (0.58), residues: 60 loop : -1.11 (0.45), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 610 TYR 0.015 0.002 TYR A 221 PHE 0.018 0.002 PHE A 100 TRP 0.011 0.002 TRP A 305 HIS 0.007 0.001 HIS A 632 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.22 ( 4906) covalent geometry : angle 0.67119 / 0.35 ( 6644) hydrogen bonds : bond 0.04012 / 2.67 ( 260) hydrogen bonds : angle 4.94004 / 3.63 ( 744) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1194 Ramachandran restraints generated. 597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1194 Ramachandran restraints generated. 597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 LEU cc_start: 0.8712 (mt) cc_final: 0.8430 (mp) REVERT: A 291 ASP cc_start: 0.8175 (t0) cc_final: 0.7898 (t0) REVERT: A 295 MET cc_start: 0.8895 (tpp) cc_final: 0.8398 (tpp) REVERT: A 486 MET cc_start: 0.8582 (mmm) cc_final: 0.7022 (ttt) REVERT: A 519 MET cc_start: 0.8444 (tpt) cc_final: 0.8099 (mtt) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.0673 time to fit residues: 6.9298 Evaluate side-chains 64 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 17 optimal weight: 2.9990 chunk 26 optimal weight: 8.9990 chunk 47 optimal weight: 0.9990 chunk 11 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 27 optimal weight: 0.0470 chunk 33 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 overall best weight: 0.9682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.123470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.093909 restraints weight = 18754.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.096165 restraints weight = 12840.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.097696 restraints weight = 9728.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.098858 restraints weight = 7949.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.099646 restraints weight = 6826.337| |-----------------------------------------------------------------------------| r_work (final): 0.3918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4906 Z= 0.121 Angle : 0.570 8.703 6644 Z= 0.292 Chirality : 0.039 0.168 741 Planarity : 0.004 0.037 855 Dihedral : 4.295 17.352 651 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.36), residues: 597 helix: 1.63 (0.29), residues: 330 sheet: -0.80 (0.54), residues: 70 loop : -1.17 (0.47), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 644 TYR 0.019 0.002 TYR A 379 PHE 0.025 0.002 PHE A 593 TRP 0.015 0.001 TRP A 640 HIS 0.004 0.001 HIS A 632 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 4906) covalent geometry : angle 0.57027 / 0.29 ( 6644) hydrogen bonds : bond 0.03341 / 2.24 ( 260) hydrogen bonds : angle 4.50841 / 3.30 ( 744) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1194 Ramachandran restraints generated. 597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1194 Ramachandran restraints generated. 597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 LEU cc_start: 0.8716 (mt) cc_final: 0.8461 (mp) REVERT: A 279 CYS cc_start: 0.7122 (m) cc_final: 0.6913 (m) REVERT: A 291 ASP cc_start: 0.8127 (t0) cc_final: 0.7840 (t0) REVERT: A 295 MET cc_start: 0.8900 (tpp) cc_final: 0.8412 (tpp) REVERT: A 399 LEU cc_start: 0.7454 (mt) cc_final: 0.6946 (mp) REVERT: A 416 ASP cc_start: 0.8800 (t0) cc_final: 0.8591 (t0) REVERT: A 486 MET cc_start: 0.8533 (mmm) cc_final: 0.6971 (ttt) REVERT: A 519 MET cc_start: 0.8410 (tpt) cc_final: 0.8126 (mtt) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.0692 time to fit residues: 7.4696 Evaluate side-chains 69 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 46 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 49 optimal weight: 0.0370 chunk 10 optimal weight: 3.9990 chunk 13 optimal weight: 10.0000 chunk 19 optimal weight: 0.8980 chunk 38 optimal weight: 10.0000 overall best weight: 1.1662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 583 GLN ** 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 = 0.4235 r_free = 0.4235 target = 0.122804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.092942 restraints weight = 18819.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.095131 restraints weight = 12940.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.096693 restraints weight = 9904.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.097595 restraints weight = 8128.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.098454 restraints weight = 7144.751| |-----------------------------------------------------------------------------| r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4906 Z= 0.128 Angle : 0.570 8.638 6644 Z= 0.295 Chirality : 0.039 0.133 741 Planarity : 0.004 0.037 855 Dihedral : 4.284 17.151 651 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.36), residues: 597 helix: 1.59 (0.29), residues: 330 sheet: -0.71 (0.55), residues: 69 loop : -1.11 (0.47), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 644 TYR 0.039 0.002 TYR A 379 PHE 0.032 0.002 PHE A 100 TRP 0.017 0.002 TRP A 640 HIS 0.003 0.001 HIS A 632 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 ( 4906) covalent geometry : angle 0.56988 / 0.29 ( 6644) hydrogen bonds : bond 0.03378 / 2.24 ( 260) hydrogen bonds : angle 4.55032 / 3.31 ( 744) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1094.65 seconds wall clock time: 19 minutes 39.31 seconds (1179.31 seconds total)