Starting phenix.real_space_refine on Wed Jun 4 22:54:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hfe_34718/06_2025/8hfe_34718.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hfe_34718/06_2025/8hfe_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8hfe_34718/06_2025/8hfe_34718.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hfe_34718/06_2025/8hfe_34718.map" model { file = "/net/cci-nas-00/data/ceres_data/8hfe_34718/06_2025/8hfe_34718.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hfe_34718/06_2025/8hfe_34718.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.130 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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, 23 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1, 'water': 22} Link IDs: {None: 22} Time building chain proxies: 3.16, per 1000 atoms: 0.72 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: 1.14 Conformation dependent library (CDL) restraints added in 536.2 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: 0.50 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: 1.17 Time building geometry restraints manager: 1.34 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: 0.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.700 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (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 TRP 0.006 0.001 TRP A 128 HIS 0.005 0.001 HIS A 199 PHE 0.012 0.001 PHE A 408 TYR 0.014 0.001 TYR A 84 ARG 0.002 0.000 ARG A 512 Details of bonding type rmsd hydrogen bonds : bond 0.14508 ( 292) hydrogen bonds : angle 5.75425 ( 843) SS BOND : bond 0.00210 ( 1) SS BOND : angle 0.85558 ( 2) covalent geometry : bond 0.00468 ( 4532) covalent geometry : angle 0.66383 ( 6183) *********************** 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 : 0.505 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: 1.2336 time to fit residues: 71.9393 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 : 0.515 ------------------------------------------------------------------------------- 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 45 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 chunk 21 optimal weight: 0.2980 chunk 42 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3647 r_free = 0.3647 target = 0.127455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.103169 restraints weight = 5527.497| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.72 r_work: 0.3313 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.0972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4533 Z= 0.170 Angle : 0.568 8.731 6185 Z= 0.300 Chirality : 0.043 0.156 691 Planarity : 0.005 0.046 752 Dihedral : 6.544 59.161 603 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.40 % Favored : 97.42 % Rotamer: Outliers : 2.59 % Allowed : 11.02 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.38), residues: 542 helix: 1.49 (0.27), residues: 377 sheet: None (None), residues: 0 loop : 0.22 (0.55), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 128 HIS 0.004 0.001 HIS A 228 PHE 0.013 0.002 PHE A 110 TYR 0.017 0.002 TYR A 84 ARG 0.002 0.000 ARG A 442 Details of bonding type rmsd hydrogen bonds : bond 0.05986 ( 292) hydrogen bonds : angle 4.74775 ( 843) SS BOND : bond 0.00398 ( 1) SS BOND : angle 1.10036 ( 2) covalent geometry : bond 0.00409 ( 4532) covalent geometry : angle 0.56795 ( 6183) *********************** 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 63 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.467 Fit side-chains revert: symmetry clash REVERT: A 121 ARG cc_start: 0.8959 (OUTLIER) cc_final: 0.8334 (mmt180) REVERT: A 189 LYS cc_start: 0.8208 (mptt) cc_final: 0.7774 (mmtt) REVERT: A 268 THR cc_start: 0.8741 (OUTLIER) cc_final: 0.8383 (p) REVERT: A 341 ARG cc_start: 0.8161 (ttp-170) cc_final: 0.7959 (ttp-110) REVERT: A 581 GLN cc_start: 0.7943 (mm-40) cc_final: 0.7720 (mt0) outliers start: 12 outliers final: 6 residues processed: 58 average time/residue: 1.1395 time to fit residues: 68.9754 Evaluate side-chains 54 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.454 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 539 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.129614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.105376 restraints weight = 5534.807| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 1.72 r_work: 0.3357 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1196 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= 0.125 Angle : 0.508 6.995 6185 Z= 0.266 Chirality : 0.040 0.158 691 Planarity : 0.004 0.039 752 Dihedral : 5.791 53.534 597 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.03 % Favored : 97.79 % Rotamer: Outliers : 2.16 % Allowed : 11.88 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.38), residues: 542 helix: 1.77 (0.27), residues: 378 sheet: None (None), residues: 0 loop : 0.16 (0.54), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 128 HIS 0.002 0.001 HIS A 228 PHE 0.012 0.001 PHE A 110 TYR 0.017 0.001 TYR A 84 ARG 0.001 0.000 ARG A 512 Details of bonding type rmsd hydrogen bonds : bond 0.05086 ( 292) hydrogen bonds : angle 4.49026 ( 843) SS BOND : bond 0.00275 ( 1) SS BOND : angle 0.86119 ( 2) covalent geometry : bond 0.00282 ( 4532) covalent geometry : angle 0.50765 ( 6183) *********************** 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 61 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.486 Fit side-chains revert: symmetry clash REVERT: A 75 ASP cc_start: 0.7664 (t70) cc_final: 0.7058 (t70) REVERT: A 189 LYS cc_start: 0.8238 (mptt) cc_final: 0.7820 (mmtt) REVERT: A 254 LYS cc_start: 0.7875 (mtmt) cc_final: 0.7545 (mttt) REVERT: A 268 THR cc_start: 0.8697 (OUTLIER) cc_final: 0.8426 (p) REVERT: A 304 GLU cc_start: 0.7597 (mm-30) cc_final: 0.7365 (mm-30) REVERT: A 508 MET cc_start: 0.8660 (OUTLIER) cc_final: 0.8451 (mtm) outliers start: 10 outliers final: 4 residues processed: 57 average time/residue: 0.9797 time to fit residues: 58.6494 Evaluate side-chains 53 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.456 ------------------------------------------------------------------------------- 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 508 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 18 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 32 optimal weight: 0.4980 chunk 21 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 539 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.129656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.105359 restraints weight = 5549.590| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.72 r_work: 0.3352 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1361 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= 0.125 Angle : 0.502 6.869 6185 Z= 0.263 Chirality : 0.040 0.170 691 Planarity : 0.004 0.038 752 Dihedral : 5.047 50.111 593 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.03 % Favored : 97.79 % Rotamer: Outliers : 2.81 % Allowed : 11.45 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.38), residues: 542 helix: 1.86 (0.27), residues: 377 sheet: None (None), residues: 0 loop : 0.15 (0.53), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 128 HIS 0.002 0.001 HIS A 228 PHE 0.016 0.001 PHE A 329 TYR 0.018 0.001 TYR A 84 ARG 0.002 0.000 ARG A 512 Details of bonding type rmsd hydrogen bonds : bond 0.05048 ( 292) hydrogen bonds : angle 4.43085 ( 843) SS BOND : bond 0.00276 ( 1) SS BOND : angle 0.84351 ( 2) covalent geometry : bond 0.00283 ( 4532) covalent geometry : angle 0.50218 ( 6183) *********************** 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 63 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 0.485 Fit side-chains revert: symmetry clash REVERT: A 75 ASP cc_start: 0.7661 (t70) cc_final: 0.7073 (t70) REVERT: A 189 LYS cc_start: 0.8294 (mptt) cc_final: 0.7893 (mmtt) REVERT: A 254 LYS cc_start: 0.7927 (mtmt) cc_final: 0.7635 (mttt) REVERT: A 268 THR cc_start: 0.8697 (OUTLIER) cc_final: 0.8436 (p) REVERT: A 389 ILE cc_start: 0.8749 (OUTLIER) cc_final: 0.8546 (mp) REVERT: A 459 PHE cc_start: 0.8249 (OUTLIER) cc_final: 0.7413 (t80) outliers start: 13 outliers final: 6 residues processed: 58 average time/residue: 0.9841 time to fit residues: 59.8904 Evaluate side-chains 56 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 256 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 535 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 37 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 39 optimal weight: 0.0770 chunk 5 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 46 optimal weight: 0.5980 chunk 51 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 375 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 = 0.3686 r_free = 0.3686 target = 0.130995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.106992 restraints weight = 5652.061| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.72 r_work: 0.3357 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1463 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= 0.116 Angle : 0.486 5.896 6185 Z= 0.254 Chirality : 0.040 0.174 691 Planarity : 0.004 0.037 752 Dihedral : 4.845 46.773 593 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.03 % Favored : 97.79 % Rotamer: Outliers : 2.59 % Allowed : 12.31 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.38), residues: 542 helix: 1.95 (0.27), residues: 378 sheet: None (None), residues: 0 loop : 0.17 (0.54), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 128 HIS 0.002 0.000 HIS A 228 PHE 0.018 0.001 PHE A 329 TYR 0.018 0.001 TYR A 84 ARG 0.001 0.000 ARG A 81 Details of bonding type rmsd hydrogen bonds : bond 0.04761 ( 292) hydrogen bonds : angle 4.36554 ( 843) SS BOND : bond 0.00266 ( 1) SS BOND : angle 0.75571 ( 2) covalent geometry : bond 0.00255 ( 4532) covalent geometry : angle 0.48610 ( 6183) *********************** 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 60 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.505 Fit side-chains revert: symmetry clash REVERT: A 75 ASP cc_start: 0.7589 (t70) cc_final: 0.7048 (t70) REVERT: A 268 THR cc_start: 0.8677 (OUTLIER) cc_final: 0.8425 (p) REVERT: A 459 PHE cc_start: 0.8150 (OUTLIER) cc_final: 0.7370 (t80) REVERT: A 610 GLN cc_start: 0.8173 (OUTLIER) cc_final: 0.6740 (mt0) outliers start: 12 outliers final: 7 residues processed: 56 average time/residue: 1.1780 time to fit residues: 69.4996 Evaluate side-chains 58 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 225 SER 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 459 PHE Chi-restraints excluded: chain A residue 535 VAL 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 9 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 13 optimal weight: 9.9990 chunk 15 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 539 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.129587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.105604 restraints weight = 5566.130| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.70 r_work: 0.3332 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4533 Z= 0.137 Angle : 0.508 6.059 6185 Z= 0.267 Chirality : 0.041 0.182 691 Planarity : 0.004 0.037 752 Dihedral : 4.816 43.919 593 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.21 % Favored : 97.60 % Rotamer: Outliers : 2.59 % Allowed : 13.17 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.37), residues: 542 helix: 1.90 (0.27), residues: 377 sheet: None (None), residues: 0 loop : 0.14 (0.53), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 128 HIS 0.002 0.001 HIS A 228 PHE 0.019 0.001 PHE A 329 TYR 0.019 0.001 TYR A 391 ARG 0.002 0.000 ARG A 81 Details of bonding type rmsd hydrogen bonds : bond 0.05278 ( 292) hydrogen bonds : angle 4.46353 ( 843) SS BOND : bond 0.00339 ( 1) SS BOND : angle 0.83810 ( 2) covalent geometry : bond 0.00318 ( 4532) covalent geometry : angle 0.50764 ( 6183) *********************** 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 63 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.457 Fit side-chains revert: symmetry clash REVERT: A 75 ASP cc_start: 0.7703 (t70) cc_final: 0.7086 (t70) REVERT: A 100 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8341 (tm) REVERT: A 121 ARG cc_start: 0.8850 (OUTLIER) cc_final: 0.8082 (mmt180) REVERT: A 268 THR cc_start: 0.8692 (OUTLIER) cc_final: 0.8441 (p) REVERT: A 610 GLN cc_start: 0.8204 (OUTLIER) cc_final: 0.6819 (mt0) outliers start: 12 outliers final: 6 residues processed: 59 average time/residue: 1.1372 time to fit residues: 70.1658 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 : 0.505 ------------------------------------------------------------------------------- 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 256 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 303 LYS 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 39 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 15 optimal weight: 0.4980 chunk 23 optimal weight: 0.0070 chunk 52 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 21 optimal weight: 4.9990 overall best weight: 0.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.130164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.106198 restraints weight = 5568.901| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.71 r_work: 0.3343 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4533 Z= 0.130 Angle : 0.502 5.839 6185 Z= 0.264 Chirality : 0.040 0.190 691 Planarity : 0.004 0.037 752 Dihedral : 4.740 41.201 593 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.85 % Favored : 97.97 % Rotamer: Outliers : 3.02 % Allowed : 12.96 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.38), residues: 542 helix: 1.94 (0.27), residues: 376 sheet: None (None), residues: 0 loop : 0.16 (0.53), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 128 HIS 0.002 0.001 HIS A 228 PHE 0.020 0.001 PHE A 329 TYR 0.020 0.001 TYR A 391 ARG 0.001 0.000 ARG A 81 Details of bonding type rmsd hydrogen bonds : bond 0.05068 ( 292) hydrogen bonds : angle 4.43198 ( 843) SS BOND : bond 0.00322 ( 1) SS BOND : angle 0.82302 ( 2) covalent geometry : bond 0.00298 ( 4532) covalent geometry : angle 0.50225 ( 6183) *********************** 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 60 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 46 time to evaluate : 0.479 Fit side-chains revert: symmetry clash REVERT: A 75 ASP cc_start: 0.7655 (t70) cc_final: 0.7042 (t70) REVERT: A 100 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8306 (tm) REVERT: A 121 ARG cc_start: 0.8827 (OUTLIER) cc_final: 0.8050 (mmt180) REVERT: A 268 THR cc_start: 0.8674 (OUTLIER) cc_final: 0.8426 (p) REVERT: A 459 PHE cc_start: 0.8268 (OUTLIER) cc_final: 0.7429 (t80) REVERT: A 610 GLN cc_start: 0.8197 (OUTLIER) cc_final: 0.6806 (mt0) outliers start: 14 outliers final: 6 residues processed: 56 average time/residue: 1.0224 time to fit residues: 60.0463 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 : 0.507 ------------------------------------------------------------------------------- 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 256 VAL 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 49 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 539 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.130345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.106211 restraints weight = 5587.284| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.71 r_work: 0.3353 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1553 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 5.827 6185 Z= 0.262 Chirality : 0.040 0.198 691 Planarity : 0.004 0.037 752 Dihedral : 4.618 37.630 593 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.21 % Favored : 97.60 % Rotamer: Outliers : 2.81 % Allowed : 13.39 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.38), residues: 542 helix: 1.96 (0.27), residues: 377 sheet: None (None), residues: 0 loop : 0.06 (0.53), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 128 HIS 0.002 0.001 HIS A 228 PHE 0.021 0.001 PHE A 329 TYR 0.022 0.001 TYR A 391 ARG 0.001 0.000 ARG A 81 Details of bonding type rmsd hydrogen bonds : bond 0.05006 ( 292) hydrogen bonds : angle 4.40426 ( 843) SS BOND : bond 0.00307 ( 1) SS BOND : angle 0.80431 ( 2) covalent geometry : bond 0.00291 ( 4532) covalent geometry : angle 0.50002 ( 6183) *********************** 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 60 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 0.784 Fit side-chains revert: symmetry clash REVERT: A 75 ASP cc_start: 0.7660 (t70) cc_final: 0.7081 (t70) REVERT: A 100 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8334 (tm) REVERT: A 121 ARG cc_start: 0.8827 (OUTLIER) cc_final: 0.8035 (mmt180) REVERT: A 268 THR cc_start: 0.8676 (OUTLIER) cc_final: 0.8426 (p) REVERT: A 459 PHE cc_start: 0.8256 (OUTLIER) cc_final: 0.7445 (t80) REVERT: A 579 SER cc_start: 0.8225 (m) cc_final: 0.7968 (p) REVERT: A 610 GLN cc_start: 0.8172 (OUTLIER) cc_final: 0.6802 (mt0) outliers start: 13 outliers final: 6 residues processed: 56 average time/residue: 1.5529 time to fit residues: 90.6019 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 : 0.518 ------------------------------------------------------------------------------- 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 256 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 41 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 11 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 42 optimal weight: 0.0980 chunk 48 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 539 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.131374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.107460 restraints weight = 5534.160| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 1.70 r_work: 0.3380 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1636 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= 0.116 Angle : 0.492 6.862 6185 Z= 0.255 Chirality : 0.040 0.206 691 Planarity : 0.004 0.036 752 Dihedral : 4.502 33.717 593 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.21 % Favored : 97.60 % Rotamer: Outliers : 2.38 % Allowed : 14.04 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.38), residues: 542 helix: 2.02 (0.27), residues: 377 sheet: None (None), residues: 0 loop : 0.08 (0.53), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 128 HIS 0.002 0.000 HIS A 228 PHE 0.024 0.001 PHE A 329 TYR 0.026 0.001 TYR A 391 ARG 0.001 0.000 ARG A 512 Details of bonding type rmsd hydrogen bonds : bond 0.04686 ( 292) hydrogen bonds : angle 4.36537 ( 843) SS BOND : bond 0.00275 ( 1) SS BOND : angle 0.78901 ( 2) covalent geometry : bond 0.00256 ( 4532) covalent geometry : angle 0.49193 ( 6183) *********************** 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: 11 poor density : 45 time to evaluate : 0.460 Fit side-chains revert: symmetry clash REVERT: A 75 ASP cc_start: 0.7652 (t70) cc_final: 0.7126 (t70) REVERT: A 100 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8273 (tm) REVERT: A 121 ARG cc_start: 0.8778 (OUTLIER) cc_final: 0.7979 (mmt180) REVERT: A 189 LYS cc_start: 0.8382 (mptt) cc_final: 0.7951 (mmtt) REVERT: A 268 THR cc_start: 0.8649 (OUTLIER) cc_final: 0.8375 (p) REVERT: A 459 PHE cc_start: 0.8112 (OUTLIER) cc_final: 0.7343 (t80) REVERT: A 579 SER cc_start: 0.8185 (m) cc_final: 0.7923 (p) REVERT: A 610 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.6712 (mt0) outliers start: 11 outliers final: 6 residues processed: 52 average time/residue: 1.0362 time to fit residues: 56.6468 Evaluate side-chains 54 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.498 ------------------------------------------------------------------------------- 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 256 VAL 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 508 MET 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 26 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 13 optimal weight: 7.9990 chunk 44 optimal weight: 0.1980 chunk 45 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 16 optimal weight: 0.0970 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 539 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.132108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.108418 restraints weight = 5514.398| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 1.69 r_work: 0.3381 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1722 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= 0.114 Angle : 0.492 6.554 6185 Z= 0.254 Chirality : 0.039 0.212 691 Planarity : 0.004 0.038 752 Dihedral : 4.448 30.611 593 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.03 % Favored : 97.79 % Rotamer: Outliers : 2.81 % Allowed : 14.47 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.38), residues: 542 helix: 2.09 (0.27), residues: 375 sheet: None (None), residues: 0 loop : -0.00 (0.53), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 553 HIS 0.002 0.000 HIS A 228 PHE 0.025 0.001 PHE A 329 TYR 0.037 0.001 TYR A 391 ARG 0.001 0.000 ARG A 512 Details of bonding type rmsd hydrogen bonds : bond 0.04599 ( 292) hydrogen bonds : angle 4.34446 ( 843) SS BOND : bond 0.00251 ( 1) SS BOND : angle 0.75568 ( 2) covalent geometry : bond 0.00250 ( 4532) covalent geometry : angle 0.49214 ( 6183) ********************** 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 57 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 44 time to evaluate : 0.662 Fit side-chains revert: symmetry clash REVERT: A 75 ASP cc_start: 0.7576 (t70) cc_final: 0.7056 (t70) REVERT: A 100 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8282 (tm) REVERT: A 121 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.7944 (mmt180) REVERT: A 189 LYS cc_start: 0.8376 (mptt) cc_final: 0.7947 (mmtt) REVERT: A 242 MET cc_start: 0.8560 (mtp) cc_final: 0.8280 (mtm) REVERT: A 268 THR cc_start: 0.8656 (OUTLIER) cc_final: 0.8373 (p) REVERT: A 459 PHE cc_start: 0.8090 (OUTLIER) cc_final: 0.7348 (t80) REVERT: A 579 SER cc_start: 0.8182 (m) cc_final: 0.7916 (p) REVERT: A 610 GLN cc_start: 0.8003 (OUTLIER) cc_final: 0.6639 (mt0) outliers start: 13 outliers final: 7 residues processed: 53 average time/residue: 1.1174 time to fit residues: 61.9663 Evaluate side-chains 56 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.504 ------------------------------------------------------------------------------- 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 256 VAL 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 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 22 optimal weight: 5.9990 chunk 7 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 29 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 539 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.128090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.104028 restraints weight = 5545.933| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.69 r_work: 0.3312 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4533 Z= 0.169 Angle : 0.551 6.646 6185 Z= 0.289 Chirality : 0.042 0.205 691 Planarity : 0.004 0.038 752 Dihedral : 4.612 27.007 593 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.58 % Favored : 97.23 % Rotamer: Outliers : 2.16 % Allowed : 15.12 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.37), residues: 542 helix: 1.89 (0.27), residues: 376 sheet: None (None), residues: 0 loop : 0.02 (0.52), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 556 HIS 0.003 0.001 HIS A 228 PHE 0.025 0.002 PHE A 329 TYR 0.019 0.002 TYR A 84 ARG 0.003 0.000 ARG A 81 Details of bonding type rmsd hydrogen bonds : bond 0.05796 ( 292) hydrogen bonds : angle 4.55166 ( 843) SS BOND : bond 0.00419 ( 1) SS BOND : angle 0.90851 ( 2) covalent geometry : bond 0.00409 ( 4532) covalent geometry : angle 0.55101 ( 6183) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3839.16 seconds wall clock time: 68 minutes 28.34 seconds (4108.34 seconds total)