Starting phenix.real_space_refine on Wed Jul 1 23:54:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hfe_34718/07_2026/8hfe_34718.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hfe_34718/07_2026/8hfe_34718.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hfe_34718/07_2026/8hfe_34718.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hfe_34718/07_2026/8hfe_34718.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hfe_34718/07_2026/8hfe_34718.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hfe_34718/07_2026/8hfe_34718.map" } resolution = 2.5 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= 0.130 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: 5 Type Number sf(0) Gaussians S 20 5.16 5 Cl 1 4.86 5 C 2948 2.51 5 N 682 2.21 5 O 762 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4413 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 4390 Classifications: {'peptide': 548} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 528} Chain breaks: 2 Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 22 Ad-hoc single atom residues: {' CL': 1} Classifications: {'water': 22} Link IDs: {None: 21} Chain breaks: 1 Time building chain proxies: 1.24, per 1000 atoms: 0.28 Number of scatterers: 4413 At special positions: 0 Unit cell: (70.3625, 71.445, 99.59, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 20 16.00 O 762 8.00 N 682 7.00 C 2948 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 176 " - pdb=" SG CYS A 185 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.36 Conformation dependent library (CDL) restraints added in 143.3 milliseconds 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1010 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 1 sheets defined 80.1% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'A' and resid 60 through 74 removed outlier: 3.511A pdb=" N ASP A 64 " --> pdb=" O GLY A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 89 removed outlier: 3.697A pdb=" N VAL A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N PHE A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) Proline residue: A 83 - end of helix Processing helix chain 'A' and resid 94 through 105 Processing helix chain 'A' and resid 105 through 121 Processing helix chain 'A' and resid 125 through 130 removed outlier: 3.696A pdb=" N ILE A 130 " --> pdb=" O VAL A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 133 No H-bonds generated for 'chain 'A' and resid 131 through 133' Processing helix chain 'A' and resid 134 through 166 removed outlier: 3.839A pdb=" N PHE A 150 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N TYR A 151 " --> pdb=" O TYR A 147 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL A 154 " --> pdb=" O PHE A 150 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE A 156 " --> pdb=" O TYR A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 217 Processing helix chain 'A' and resid 220 through 224 Processing helix chain 'A' and resid 234 through 253 Processing helix chain 'A' and resid 264 through 283 removed outlier: 3.758A pdb=" N THR A 268 " --> pdb=" O TRP A 264 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU A 269 " --> pdb=" O ILE A 265 " (cutoff:3.500A) Proline residue: A 270 - end of helix removed outlier: 3.956A pdb=" N THR A 283 " --> pdb=" O VAL A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 295 removed outlier: 3.515A pdb=" N GLY A 290 " --> pdb=" O GLY A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 303 removed outlier: 3.556A pdb=" N LEU A 302 " --> pdb=" O ASP A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 320 Processing helix chain 'A' and resid 324 through 331 Processing helix chain 'A' and resid 338 through 373 Processing helix chain 'A' and resid 385 through 396 Proline residue: A 392 - end of helix Processing helix chain 'A' and resid 400 through 435 removed outlier: 3.552A pdb=" N ASP A 434 " --> pdb=" O GLY A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 440 Processing helix chain 'A' and resid 441 through 459 Processing helix chain 'A' and resid 464 through 476 removed outlier: 3.623A pdb=" N VAL A 468 " --> pdb=" O GLY A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 494 Processing helix chain 'A' and resid 497 through 510 Processing helix chain 'A' and resid 514 through 523 Processing helix chain 'A' and resid 523 through 539 Processing helix chain 'A' and resid 551 through 567 removed outlier: 3.806A pdb=" N ASN A 555 " --> pdb=" O PRO A 551 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N SER A 565 " --> pdb=" O ILE A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 580 Processing helix chain 'A' and resid 583 through 593 Processing helix chain 'A' and resid 594 through 604 removed outlier: 3.652A pdb=" N HIS A 598 " --> pdb=" O GLU A 595 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N HIS A 599 " --> pdb=" O ASN A 596 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA A 602 " --> pdb=" O HIS A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 609 Processing helix chain 'A' and resid 610 through 615 removed outlier: 3.834A pdb=" N TRP A 614 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 544 through 545 292 hydrogen bonds defined for protein. 843 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: 0.42 Time building geometry restraints manager: 0.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 649 1.28 - 1.41: 1336 1.41 - 1.55: 2516 1.55 - 1.68: 0 1.68 - 1.81: 31 Bond restraints: 4532 Sorted by residual: bond pdb=" C SER A 480 " pdb=" O SER A 480 " ideal model delta sigma weight residual 1.236 1.143 0.093 1.19e-02 7.06e+03 6.06e+01 bond pdb=" C GLY A 478 " pdb=" O GLY A 478 " ideal model delta sigma weight residual 1.235 1.145 0.090 1.35e-02 5.49e+03 4.46e+01 bond pdb=" CA SER A 480 " pdb=" CB SER A 480 " ideal model delta sigma weight residual 1.530 1.431 0.099 1.63e-02 3.76e+03 3.70e+01 bond pdb=" CA ALA A 477 " pdb=" CB ALA A 477 " ideal model delta sigma weight residual 1.530 1.472 0.058 9.80e-03 1.04e+04 3.51e+01 bond pdb=" C ALA A 476 " pdb=" O ALA A 476 " ideal model delta sigma weight residual 1.236 1.179 0.057 1.32e-02 5.74e+03 1.87e+01 ... (remaining 4527 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 6109 2.51 - 5.02: 61 5.02 - 7.54: 12 7.54 - 10.05: 0 10.05 - 12.56: 1 Bond angle restraints: 6183 Sorted by residual: angle pdb=" C GLU A 425 " pdb=" N ALA A 426 " pdb=" CA ALA A 426 " ideal model delta sigma weight residual 120.38 132.94 -12.56 1.37e+00 5.33e-01 8.41e+01 angle pdb=" CA ALA A 426 " pdb=" C ALA A 426 " pdb=" O ALA A 426 " ideal model delta sigma weight residual 120.63 125.86 -5.23 1.08e+00 8.57e-01 2.34e+01 angle pdb=" CA ALA A 477 " pdb=" C ALA A 477 " pdb=" N GLY A 478 " ideal model delta sigma weight residual 115.78 121.39 -5.61 1.35e+00 5.49e-01 1.72e+01 angle pdb=" O PHE A 475 " pdb=" C PHE A 475 " pdb=" N ALA A 476 " ideal model delta sigma weight residual 122.48 117.47 5.01 1.21e+00 6.83e-01 1.71e+01 angle pdb=" CA PHE A 475 " pdb=" C PHE A 475 " pdb=" N ALA A 476 " ideal model delta sigma weight residual 118.47 123.63 -5.16 1.26e+00 6.30e-01 1.68e+01 ... (remaining 6178 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.54: 2208 15.54 - 31.08: 229 31.08 - 46.62: 71 46.62 - 62.16: 22 62.16 - 77.70: 2 Dihedral angle restraints: 2532 sinusoidal: 947 harmonic: 1585 Sorted by residual: dihedral pdb=" CA ILE A 103 " pdb=" C ILE A 103 " pdb=" N ILE A 104 " pdb=" CA ILE A 104 " ideal model delta harmonic sigma weight residual -180.00 -156.47 -23.53 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" C TYR A 205 " pdb=" N TYR A 205 " pdb=" CA TYR A 205 " pdb=" CB TYR A 205 " ideal model delta harmonic sigma weight residual -122.60 -132.76 10.16 0 2.50e+00 1.60e-01 1.65e+01 dihedral pdb=" N TYR A 205 " pdb=" C TYR A 205 " pdb=" CA TYR A 205 " pdb=" CB TYR A 205 " ideal model delta harmonic sigma weight residual 122.80 132.51 -9.71 0 2.50e+00 1.60e-01 1.51e+01 ... (remaining 2529 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 662 0.088 - 0.175: 26 0.175 - 0.263: 2 0.263 - 0.350: 0 0.350 - 0.438: 1 Chirality restraints: 691 Sorted by residual: chirality pdb=" CA TYR A 205 " pdb=" N TYR A 205 " pdb=" C TYR A 205 " pdb=" CB TYR A 205 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.79e+00 chirality pdb=" CA ILE A 617 " pdb=" N ILE A 617 " pdb=" C ILE A 617 " pdb=" CB ILE A 617 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA SER A 480 " pdb=" N SER A 480 " pdb=" C SER A 480 " pdb=" CB SER A 480 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.14e-01 ... (remaining 688 not shown) Planarity restraints: 752 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 103 " 0.019 2.00e-02 2.50e+03 3.84e-02 1.47e+01 pdb=" C ILE A 103 " -0.066 2.00e-02 2.50e+03 pdb=" O ILE A 103 " 0.025 2.00e-02 2.50e+03 pdb=" N ILE A 104 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 475 " 0.012 2.00e-02 2.50e+03 2.25e-02 5.07e+00 pdb=" C PHE A 475 " -0.039 2.00e-02 2.50e+03 pdb=" O PHE A 475 " 0.014 2.00e-02 2.50e+03 pdb=" N ALA A 476 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 426 " -0.011 2.00e-02 2.50e+03 2.13e-02 4.53e+00 pdb=" C ALA A 426 " 0.037 2.00e-02 2.50e+03 pdb=" O ALA A 426 " -0.015 2.00e-02 2.50e+03 pdb=" N VAL A 427 " -0.011 2.00e-02 2.50e+03 ... (remaining 749 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 50 2.65 - 3.21: 4149 3.21 - 3.77: 7111 3.77 - 4.34: 10113 4.34 - 4.90: 16559 Nonbonded interactions: 37982 Sorted by model distance: nonbonded pdb=" OE1 GLU A 113 " pdb=" O HOH A 801 " model vdw 2.082 3.040 nonbonded pdb=" O ALA A 384 " pdb=" O HOH A 802 " model vdw 2.090 3.040 nonbonded pdb=" O HOH A 813 " pdb=" O HOH A 822 " model vdw 2.154 3.040 nonbonded pdb=" O HOH A 814 " pdb=" O HOH A 817 " model vdw 2.164 3.040 nonbonded pdb=" OE2 GLU A 488 " pdb=" O HOH A 803 " model vdw 2.211 3.040 ... (remaining 37977 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: 0.410 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.480 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:6.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 4533 Z= 0.305 Angle : 0.664 12.562 6185 Z= 0.404 Chirality : 0.042 0.438 691 Planarity : 0.004 0.045 752 Dihedral : 14.852 77.702 1519 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.58 % Favored : 97.23 % Rotamer: Outliers : 1.08 % Allowed : 11.88 % Favored : 87.04 % 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: 1.37 (0.38), residues: 542 helix: 1.34 (0.28), residues: 372 sheet: None (None), residues: 0 loop : 0.12 (0.53), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 512 TYR 0.014 0.001 TYR A 84 PHE 0.012 0.001 PHE A 408 TRP 0.006 0.001 TRP A 128 HIS 0.005 0.001 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.31 ( 4532) covalent geometry : angle 0.66383 / 0.40 ( 6183) SS BOND : bond 0.00210 / 0.13 ( 1) SS BOND : angle 0.85558 / 0.35 ( 2) hydrogen bonds : bond 0.14508 / 9.36 ( 292) hydrogen bonds : angle 5.75425 / 4.08 ( 843) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.178 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 254 LYS cc_start: 0.7944 (mtmt) cc_final: 0.7653 (mttt) outliers start: 5 outliers final: 4 residues processed: 56 average time/residue: 0.5384 time to fit residues: 31.3531 Evaluate side-chains 52 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LYS Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain A residue 350 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.4980 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 0.3980 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 280 HIS A 539 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.130759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.106849 restraints weight = 5567.164| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.73 r_work: 0.3378 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4533 Z= 0.124 Angle : 0.524 7.943 6185 Z= 0.272 Chirality : 0.040 0.155 691 Planarity : 0.004 0.039 752 Dihedral : 6.351 58.242 603 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.03 % Favored : 97.79 % Rotamer: Outliers : 2.59 % Allowed : 10.58 % Favored : 86.83 % 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: 1.80 (0.38), residues: 542 helix: 1.61 (0.27), residues: 379 sheet: None (None), residues: 0 loop : 0.36 (0.57), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 442 TYR 0.015 0.001 TYR A 84 PHE 0.013 0.001 PHE A 110 TRP 0.009 0.001 TRP A 128 HIS 0.002 0.001 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 4532) covalent geometry : angle 0.52392 / 0.27 ( 6183) SS BOND : bond 0.00271 / 0.17 ( 1) SS BOND : angle 0.87821 / 0.37 ( 2) hydrogen bonds : bond 0.05065 / 3.38 ( 292) hydrogen bonds : angle 4.57184 / 3.23 ( 843) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.101 Fit side-chains revert: symmetry clash REVERT: A 75 ASP cc_start: 0.7573 (t70) cc_final: 0.6993 (t70) REVERT: A 254 LYS cc_start: 0.7820 (mtmt) cc_final: 0.7541 (mttt) REVERT: A 268 THR cc_start: 0.8723 (OUTLIER) cc_final: 0.8434 (p) REVERT: A 459 PHE cc_start: 0.8115 (OUTLIER) cc_final: 0.7300 (t80) outliers start: 12 outliers final: 6 residues processed: 61 average time/residue: 0.4382 time to fit residues: 27.8901 Evaluate side-chains 56 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 459 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 0.7980 chunk 44 optimal weight: 0.1980 chunk 10 optimal weight: 1.9990 chunk 36 optimal weight: 0.0980 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 6 optimal weight: 0.0570 chunk 9 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 overall best weight: 0.3898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 153 ASN A 539 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.133619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.109757 restraints weight = 5533.278| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 1.73 r_work: 0.3410 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4533 Z= 0.107 Angle : 0.477 6.056 6185 Z= 0.247 Chirality : 0.039 0.164 691 Planarity : 0.004 0.032 752 Dihedral : 5.025 52.220 593 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.21 % Favored : 97.60 % Rotamer: Outliers : 1.94 % Allowed : 11.88 % Favored : 86.18 % 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: 2.15 (0.38), residues: 542 helix: 1.95 (0.27), residues: 378 sheet: None (None), residues: 0 loop : 0.27 (0.55), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 512 TYR 0.016 0.001 TYR A 84 PHE 0.014 0.001 PHE A 329 TRP 0.007 0.001 TRP A 553 HIS 0.002 0.000 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.11 ( 4532) covalent geometry : angle 0.47659 / 0.25 ( 6183) SS BOND : bond 0.00194 / 0.12 ( 1) SS BOND : angle 0.69959 / 0.29 ( 2) hydrogen bonds : bond 0.04433 / 2.97 ( 292) hydrogen bonds : angle 4.28901 / 3.03 ( 843) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.163 Fit side-chains revert: symmetry clash REVERT: A 75 ASP cc_start: 0.7495 (t70) cc_final: 0.7046 (t70) REVERT: A 121 ARG cc_start: 0.8838 (OUTLIER) cc_final: 0.8207 (mmt180) REVERT: A 268 THR cc_start: 0.8759 (OUTLIER) cc_final: 0.8504 (p) REVERT: A 459 PHE cc_start: 0.7968 (OUTLIER) cc_final: 0.7200 (t80) REVERT: A 539 ASN cc_start: 0.8567 (m-40) cc_final: 0.8362 (m110) outliers start: 9 outliers final: 3 residues processed: 54 average time/residue: 0.4655 time to fit residues: 26.2547 Evaluate side-chains 49 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain A residue 459 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 50 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 48 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3660 r_free = 0.3660 target = 0.128645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.104112 restraints weight = 5558.056| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.73 r_work: 0.3327 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4533 Z= 0.152 Angle : 0.529 7.358 6185 Z= 0.278 Chirality : 0.042 0.161 691 Planarity : 0.004 0.036 752 Dihedral : 5.098 50.272 593 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.03 % Favored : 97.79 % Rotamer: Outliers : 2.81 % Allowed : 12.53 % Favored : 84.67 % 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: 2.01 (0.38), residues: 542 helix: 1.87 (0.27), residues: 377 sheet: None (None), residues: 0 loop : 0.18 (0.53), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 81 TYR 0.018 0.002 TYR A 84 PHE 0.016 0.002 PHE A 329 TRP 0.007 0.001 TRP A 253 HIS 0.003 0.001 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 ( 4532) covalent geometry : angle 0.52919 / 0.28 ( 6183) SS BOND : bond 0.00366 / 0.23 ( 1) SS BOND : angle 0.86421 / 0.35 ( 2) hydrogen bonds : bond 0.05592 / 3.73 ( 292) hydrogen bonds : angle 4.48067 / 3.18 ( 843) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 49 time to evaluate : 0.101 Fit side-chains revert: symmetry clash REVERT: A 121 ARG cc_start: 0.8938 (OUTLIER) cc_final: 0.8290 (mmt180) REVERT: A 254 LYS cc_start: 0.8040 (mtmt) cc_final: 0.7719 (mttt) REVERT: A 268 THR cc_start: 0.8700 (OUTLIER) cc_final: 0.8433 (p) REVERT: A 581 GLN cc_start: 0.7836 (mm-40) cc_final: 0.7610 (mt0) outliers start: 13 outliers final: 5 residues processed: 58 average time/residue: 0.4886 time to fit residues: 29.4777 Evaluate side-chains 54 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain A residue 399 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 51 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 23 optimal weight: 0.3980 chunk 38 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 539 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.130108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.105809 restraints weight = 5595.244| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.73 r_work: 0.3348 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4533 Z= 0.126 Angle : 0.502 6.196 6185 Z= 0.263 Chirality : 0.040 0.171 691 Planarity : 0.004 0.035 752 Dihedral : 4.926 47.608 593 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.85 % Favored : 97.97 % Rotamer: Outliers : 2.16 % Allowed : 12.53 % Favored : 85.31 % 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: 2.12 (0.38), residues: 542 helix: 1.96 (0.27), residues: 378 sheet: None (None), residues: 0 loop : 0.19 (0.53), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 512 TYR 0.019 0.001 TYR A 84 PHE 0.018 0.001 PHE A 329 TRP 0.007 0.001 TRP A 128 HIS 0.002 0.001 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 ( 4532) covalent geometry : angle 0.50189 / 0.26 ( 6183) SS BOND : bond 0.00310 / 0.19 ( 1) SS BOND : angle 0.81017 / 0.33 ( 2) hydrogen bonds : bond 0.05054 / 3.39 ( 292) hydrogen bonds : angle 4.41784 / 3.13 ( 843) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.176 Fit side-chains revert: symmetry clash REVERT: A 75 ASP cc_start: 0.7650 (t70) cc_final: 0.7089 (t70) REVERT: A 121 ARG cc_start: 0.8928 (OUTLIER) cc_final: 0.8264 (mmt180) REVERT: A 254 LYS cc_start: 0.7882 (mtmt) cc_final: 0.7597 (mttt) REVERT: A 268 THR cc_start: 0.8704 (OUTLIER) cc_final: 0.8448 (p) REVERT: A 581 GLN cc_start: 0.7845 (mm-40) cc_final: 0.7636 (mt0) REVERT: A 610 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.6808 (mt0) outliers start: 10 outliers final: 5 residues processed: 52 average time/residue: 0.4887 time to fit residues: 26.4859 Evaluate side-chains 53 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 610 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 43 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 44 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 539 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.130397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.106231 restraints weight = 5652.897| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.73 r_work: 0.3340 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4533 Z= 0.127 Angle : 0.500 5.856 6185 Z= 0.262 Chirality : 0.040 0.182 691 Planarity : 0.004 0.035 752 Dihedral : 4.775 43.603 593 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.03 % Favored : 97.79 % Rotamer: Outliers : 2.38 % Allowed : 12.96 % Favored : 84.67 % 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: 2.15 (0.38), residues: 542 helix: 1.98 (0.27), residues: 378 sheet: None (None), residues: 0 loop : 0.20 (0.54), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 81 TYR 0.020 0.001 TYR A 391 PHE 0.019 0.001 PHE A 329 TRP 0.007 0.001 TRP A 128 HIS 0.002 0.001 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 ( 4532) covalent geometry : angle 0.49966 / 0.26 ( 6183) SS BOND : bond 0.00311 / 0.19 ( 1) SS BOND : angle 0.80803 / 0.33 ( 2) hydrogen bonds : bond 0.05053 / 3.39 ( 292) hydrogen bonds : angle 4.39187 / 3.12 ( 843) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.095 Fit side-chains revert: symmetry clash REVERT: A 75 ASP cc_start: 0.7636 (t70) cc_final: 0.7080 (t70) REVERT: A 100 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8303 (tm) REVERT: A 121 ARG cc_start: 0.8928 (OUTLIER) cc_final: 0.8270 (mmt180) REVERT: A 254 LYS cc_start: 0.7909 (mtmt) cc_final: 0.7678 (mttt) REVERT: A 268 THR cc_start: 0.8649 (OUTLIER) cc_final: 0.8401 (p) REVERT: A 304 GLU cc_start: 0.7594 (mm-30) cc_final: 0.7324 (mm-30) REVERT: A 459 PHE cc_start: 0.8261 (OUTLIER) cc_final: 0.7431 (t80) REVERT: A 581 GLN cc_start: 0.7874 (mm-40) cc_final: 0.7668 (mt0) REVERT: A 610 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.6763 (mt0) outliers start: 11 outliers final: 5 residues processed: 56 average time/residue: 0.4455 time to fit residues: 25.9888 Evaluate side-chains 57 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 610 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 39 optimal weight: 0.4980 chunk 47 optimal weight: 4.9990 chunk 3 optimal weight: 0.5980 chunk 40 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 539 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.131240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.107175 restraints weight = 5542.878| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.71 r_work: 0.3371 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4533 Z= 0.120 Angle : 0.490 5.807 6185 Z= 0.256 Chirality : 0.040 0.190 691 Planarity : 0.004 0.034 752 Dihedral : 4.644 39.955 593 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.85 % Favored : 97.97 % Rotamer: Outliers : 2.59 % Allowed : 12.96 % Favored : 84.45 % 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: 2.22 (0.38), residues: 542 helix: 2.03 (0.27), residues: 378 sheet: None (None), residues: 0 loop : 0.24 (0.54), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 512 TYR 0.022 0.001 TYR A 391 PHE 0.020 0.001 PHE A 329 TRP 0.007 0.001 TRP A 128 HIS 0.002 0.000 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 ( 4532) covalent geometry : angle 0.48998 / 0.26 ( 6183) SS BOND : bond 0.00290 / 0.18 ( 1) SS BOND : angle 0.77939 / 0.32 ( 2) hydrogen bonds : bond 0.04833 / 3.24 ( 292) hydrogen bonds : angle 4.35447 / 3.10 ( 843) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 49 time to evaluate : 0.119 Fit side-chains revert: symmetry clash REVERT: A 75 ASP cc_start: 0.7556 (t70) cc_final: 0.7023 (t70) REVERT: A 100 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8289 (tm) REVERT: A 121 ARG cc_start: 0.8916 (OUTLIER) cc_final: 0.8245 (mmt180) REVERT: A 242 MET cc_start: 0.8521 (mtp) cc_final: 0.8174 (mtm) REVERT: A 268 THR cc_start: 0.8663 (OUTLIER) cc_final: 0.8409 (p) REVERT: A 304 GLU cc_start: 0.7581 (mm-30) cc_final: 0.7341 (mm-30) REVERT: A 459 PHE cc_start: 0.8168 (OUTLIER) cc_final: 0.7392 (t80) REVERT: A 610 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.6762 (mt0) outliers start: 12 outliers final: 5 residues processed: 58 average time/residue: 0.4548 time to fit residues: 27.4671 Evaluate side-chains 57 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 610 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 9 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 4 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 539 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.128942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.104790 restraints weight = 5607.686| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.71 r_work: 0.3322 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4533 Z= 0.153 Angle : 0.531 5.952 6185 Z= 0.280 Chirality : 0.042 0.194 691 Planarity : 0.004 0.035 752 Dihedral : 4.697 36.144 593 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.21 % Favored : 97.60 % Rotamer: Outliers : 2.38 % Allowed : 13.61 % Favored : 84.02 % 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: 2.07 (0.37), residues: 542 helix: 1.94 (0.27), residues: 376 sheet: None (None), residues: 0 loop : 0.15 (0.53), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 81 TYR 0.026 0.002 TYR A 391 PHE 0.022 0.002 PHE A 329 TRP 0.009 0.001 TRP A 253 HIS 0.003 0.001 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.15 ( 4532) covalent geometry : angle 0.53067 / 0.28 ( 6183) SS BOND : bond 0.00391 / 0.24 ( 1) SS BOND : angle 0.87444 / 0.36 ( 2) hydrogen bonds : bond 0.05551 / 3.71 ( 292) hydrogen bonds : angle 4.44577 / 3.17 ( 843) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.161 Fit side-chains revert: symmetry clash REVERT: A 75 ASP cc_start: 0.7706 (t70) cc_final: 0.7087 (t70) REVERT: A 100 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8297 (tm) REVERT: A 121 ARG cc_start: 0.8961 (OUTLIER) cc_final: 0.8288 (mmt180) REVERT: A 242 MET cc_start: 0.8587 (mtp) cc_final: 0.8231 (mtm) REVERT: A 268 THR cc_start: 0.8680 (OUTLIER) cc_final: 0.8412 (p) REVERT: A 610 GLN cc_start: 0.8189 (OUTLIER) cc_final: 0.6839 (mt0) outliers start: 11 outliers final: 6 residues processed: 55 average time/residue: 0.5201 time to fit residues: 29.8127 Evaluate side-chains 55 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 610 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 37 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 6 optimal weight: 0.0270 chunk 28 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 19 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 539 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.131355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.107269 restraints weight = 5621.413| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.72 r_work: 0.3371 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4533 Z= 0.118 Angle : 0.496 5.790 6185 Z= 0.259 Chirality : 0.040 0.204 691 Planarity : 0.004 0.035 752 Dihedral : 4.533 33.183 593 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.40 % Favored : 97.42 % Rotamer: Outliers : 2.16 % Allowed : 14.25 % Favored : 83.59 % 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: 2.22 (0.38), residues: 542 helix: 2.07 (0.27), residues: 377 sheet: None (None), residues: 0 loop : 0.14 (0.53), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 81 TYR 0.028 0.001 TYR A 391 PHE 0.023 0.001 PHE A 329 TRP 0.007 0.001 TRP A 128 HIS 0.002 0.000 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 4532) covalent geometry : angle 0.49600 / 0.26 ( 6183) SS BOND : bond 0.00286 / 0.18 ( 1) SS BOND : angle 0.79163 / 0.33 ( 2) hydrogen bonds : bond 0.04772 / 3.21 ( 292) hydrogen bonds : angle 4.34510 / 3.10 ( 843) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.102 Fit side-chains revert: symmetry clash REVERT: A 75 ASP cc_start: 0.7579 (t70) cc_final: 0.7054 (t70) REVERT: A 100 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8309 (tm) REVERT: A 121 ARG cc_start: 0.8920 (OUTLIER) cc_final: 0.8244 (mmt180) REVERT: A 189 LYS cc_start: 0.8377 (mptt) cc_final: 0.7944 (mmtt) REVERT: A 242 MET cc_start: 0.8537 (mtp) cc_final: 0.8193 (mtm) REVERT: A 268 THR cc_start: 0.8686 (OUTLIER) cc_final: 0.8415 (p) REVERT: A 610 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.6772 (mt0) outliers start: 10 outliers final: 6 residues processed: 53 average time/residue: 0.4770 time to fit residues: 26.3579 Evaluate side-chains 54 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 610 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 30 optimal weight: 0.1980 chunk 20 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 46 optimal weight: 0.6980 chunk 19 optimal weight: 0.0970 chunk 48 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 47 optimal weight: 0.0970 chunk 29 optimal weight: 0.9990 overall best weight: 0.3576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 539 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.133763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.109932 restraints weight = 5568.327| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.71 r_work: 0.3422 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 4533 Z= 0.108 Angle : 0.481 5.701 6185 Z= 0.249 Chirality : 0.039 0.210 691 Planarity : 0.004 0.038 752 Dihedral : 4.425 30.078 593 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.03 % Favored : 97.79 % Rotamer: Outliers : 1.94 % Allowed : 14.69 % Favored : 83.37 % 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: 2.28 (0.38), residues: 542 helix: 2.15 (0.27), residues: 376 sheet: None (None), residues: 0 loop : 0.07 (0.53), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 512 TYR 0.037 0.001 TYR A 391 PHE 0.024 0.001 PHE A 329 TRP 0.008 0.001 TRP A 553 HIS 0.001 0.000 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.11 ( 4532) covalent geometry : angle 0.48063 / 0.25 ( 6183) SS BOND : bond 0.00220 / 0.14 ( 1) SS BOND : angle 0.71820 / 0.30 ( 2) hydrogen bonds : bond 0.04354 / 2.92 ( 292) hydrogen bonds : angle 4.27220 / 3.06 ( 843) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.165 Fit side-chains revert: symmetry clash REVERT: A 75 ASP cc_start: 0.7457 (t70) cc_final: 0.7137 (t70) REVERT: A 100 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8263 (tm) REVERT: A 121 ARG cc_start: 0.8840 (OUTLIER) cc_final: 0.8158 (mmt180) REVERT: A 189 LYS cc_start: 0.8370 (mptt) cc_final: 0.7940 (mmtt) REVERT: A 242 MET cc_start: 0.8496 (mtp) cc_final: 0.8148 (mtm) REVERT: A 268 THR cc_start: 0.8636 (OUTLIER) cc_final: 0.8349 (p) REVERT: A 579 SER cc_start: 0.8162 (m) cc_final: 0.7896 (p) outliers start: 9 outliers final: 5 residues processed: 50 average time/residue: 0.5027 time to fit residues: 26.2845 Evaluate side-chains 51 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain A residue 535 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 22 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 51 optimal weight: 0.0270 chunk 6 optimal weight: 0.0770 chunk 32 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 13 optimal weight: 10.0000 chunk 8 optimal weight: 0.6980 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 539 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.133166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.109485 restraints weight = 5562.236| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 1.69 r_work: 0.3417 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4533 Z= 0.110 Angle : 0.484 5.724 6185 Z= 0.251 Chirality : 0.039 0.209 691 Planarity : 0.004 0.036 752 Dihedral : 4.356 26.779 593 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.21 % Favored : 97.60 % Rotamer: Outliers : 1.94 % Allowed : 14.69 % Favored : 83.37 % 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: 2.29 (0.38), residues: 542 helix: 2.17 (0.27), residues: 376 sheet: None (None), residues: 0 loop : 0.06 (0.53), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 512 TYR 0.017 0.001 TYR A 84 PHE 0.025 0.001 PHE A 329 TRP 0.007 0.001 TRP A 553 HIS 0.002 0.000 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 ( 4532) covalent geometry : angle 0.48387 / 0.25 ( 6183) SS BOND : bond 0.00221 / 0.14 ( 1) SS BOND : angle 0.72026 / 0.30 ( 2) hydrogen bonds : bond 0.04470 / 3.00 ( 292) hydrogen bonds : angle 4.25636 / 3.05 ( 843) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1529.49 seconds wall clock time: 26 minutes 46.76 seconds (1606.76 seconds total)