Starting phenix.real_space_refine on Fri Aug 22 13:50:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uah_42064/08_2025/8uah_42064.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uah_42064/08_2025/8uah_42064.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8uah_42064/08_2025/8uah_42064.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uah_42064/08_2025/8uah_42064.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8uah_42064/08_2025/8uah_42064.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uah_42064/08_2025/8uah_42064.map" } resolution = 3.3 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= -0.001 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 2260 2.51 5 N 580 2.21 5 O 664 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3534 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 2606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2606 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 4, 'TRANS': 329} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'ARG:plan': 14} Unresolved non-hydrogen planarities: 40 Chain: "C" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 928 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 114} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 5} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 1.12, per 1000 atoms: 0.32 Number of scatterers: 3534 At special positions: 0 Unit cell: (76.529, 83.216, 73.557, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 30 16.00 O 664 8.00 N 580 7.00 C 2260 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 396 " - pdb=" SG CYS B 422 " 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: 0.28 Conformation dependent library (CDL) restraints added in 97.7 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 894 Ramachandran restraints generated. 447 Oldfield, 0 Emsley, 447 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 860 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 3 sheets defined 37.0% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'B' and resid 379 through 384 removed outlier: 3.739A pdb=" N ARG B 384 " --> pdb=" O LYS B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 404 Processing helix chain 'B' and resid 426 through 434 removed outlier: 4.204A pdb=" N ILE B 430 " --> pdb=" O SER B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 457 removed outlier: 3.853A pdb=" N LEU B 456 " --> pdb=" O THR B 452 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS B 457 " --> pdb=" O ASP B 453 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 452 through 457' Processing helix chain 'B' and resid 478 through 488 removed outlier: 3.719A pdb=" N MET B 482 " --> pdb=" O SER B 478 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL B 484 " --> pdb=" O GLU B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 509 removed outlier: 3.654A pdb=" N VAL B 508 " --> pdb=" O THR B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 555 through 563 removed outlier: 3.767A pdb=" N MET B 559 " --> pdb=" O ASN B 555 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL B 562 " --> pdb=" O VAL B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 591 removed outlier: 4.012A pdb=" N VAL B 584 " --> pdb=" O ASN B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 615 Processing helix chain 'B' and resid 633 through 642 removed outlier: 3.548A pdb=" N ALA B 639 " --> pdb=" O ALA B 635 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLN B 640 " --> pdb=" O THR B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 659 through 664 Processing helix chain 'B' and resid 681 through 688 removed outlier: 5.135A pdb=" N ARG B 686 " --> pdb=" O THR B 683 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA B 687 " --> pdb=" O LEU B 684 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR B 688 " --> pdb=" O GLU B 685 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 30 removed outlier: 3.602A pdb=" N LEU C 24 " --> pdb=" O VAL C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 56 Processing helix chain 'C' and resid 56 through 65 removed outlier: 4.121A pdb=" N ARG C 62 " --> pdb=" O TYR C 58 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLY C 65 " --> pdb=" O SER C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 85 Processing helix chain 'C' and resid 87 through 94 Processing helix chain 'C' and resid 103 through 114 Processing helix chain 'C' and resid 124 through 132 removed outlier: 3.561A pdb=" N PHE C 128 " --> pdb=" O GLN C 124 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 416 through 419 Processing sheet with id=AA2, first strand: chain 'B' and resid 520 through 522 removed outlier: 3.579A pdb=" N LEU B 545 " --> pdb=" O SER B 570 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N SER B 674 " --> pdb=" O LEU B 648 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 43 through 47 92 hydrogen bonds defined for protein. 258 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: 0.39 Time building geometry restraints manager: 0.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1046 1.33 - 1.46: 552 1.46 - 1.58: 1947 1.58 - 1.70: 1 1.70 - 1.82: 38 Bond restraints: 3584 Sorted by residual: bond pdb=" CA VAL C 20 " pdb=" C VAL C 20 " ideal model delta sigma weight residual 1.524 1.465 0.059 1.06e-02 8.90e+03 3.14e+01 bond pdb=" CA SER C 17 " pdb=" C SER C 17 " ideal model delta sigma weight residual 1.523 1.457 0.065 1.35e-02 5.49e+03 2.35e+01 bond pdb=" N LEU C 21 " pdb=" CA LEU C 21 " ideal model delta sigma weight residual 1.459 1.403 0.056 1.28e-02 6.10e+03 1.88e+01 bond pdb=" N ASN C 19 " pdb=" CA ASN C 19 " ideal model delta sigma weight residual 1.459 1.416 0.043 1.15e-02 7.56e+03 1.42e+01 bond pdb=" CA ASP C 68 " pdb=" C ASP C 68 " ideal model delta sigma weight residual 1.523 1.475 0.049 1.34e-02 5.57e+03 1.31e+01 ... (remaining 3579 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 4701 2.75 - 5.49: 95 5.49 - 8.24: 13 8.24 - 10.99: 4 10.99 - 13.73: 4 Bond angle restraints: 4817 Sorted by residual: angle pdb=" N VAL C 20 " pdb=" CA VAL C 20 " pdb=" C VAL C 20 " ideal model delta sigma weight residual 111.62 100.53 11.09 7.90e-01 1.60e+00 1.97e+02 angle pdb=" N SER C 17 " pdb=" CA SER C 17 " pdb=" C SER C 17 " ideal model delta sigma weight residual 111.82 98.42 13.40 1.16e+00 7.43e-01 1.33e+02 angle pdb=" C GLY C 69 " pdb=" N GLU C 70 " pdb=" CA GLU C 70 " ideal model delta sigma weight residual 123.07 111.14 11.93 1.46e+00 4.69e-01 6.68e+01 angle pdb=" N ALA C 67 " pdb=" CA ALA C 67 " pdb=" C ALA C 67 " ideal model delta sigma weight residual 107.20 120.93 -13.73 1.70e+00 3.46e-01 6.53e+01 angle pdb=" CA PRO B 438 " pdb=" N PRO B 438 " pdb=" CD PRO B 438 " ideal model delta sigma weight residual 112.00 103.04 8.96 1.40e+00 5.10e-01 4.09e+01 ... (remaining 4812 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.38: 1774 17.38 - 34.76: 280 34.76 - 52.14: 107 52.14 - 69.51: 27 69.51 - 86.89: 11 Dihedral angle restraints: 2199 sinusoidal: 889 harmonic: 1310 Sorted by residual: dihedral pdb=" CB CYS B 396 " pdb=" SG CYS B 396 " pdb=" SG CYS B 422 " pdb=" CB CYS B 422 " ideal model delta sinusoidal sigma weight residual 93.00 170.73 -77.73 1 1.00e+01 1.00e-02 7.56e+01 dihedral pdb=" CA VAL B 661 " pdb=" C VAL B 661 " pdb=" N GLU B 662 " pdb=" CA GLU B 662 " ideal model delta harmonic sigma weight residual 180.00 146.65 33.35 0 5.00e+00 4.00e-02 4.45e+01 dihedral pdb=" CG ARG B 614 " pdb=" CD ARG B 614 " pdb=" NE ARG B 614 " pdb=" CZ ARG B 614 " ideal model delta sinusoidal sigma weight residual 90.00 10.35 79.65 2 1.50e+01 4.44e-03 2.06e+01 ... (remaining 2196 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 363 0.037 - 0.075: 148 0.075 - 0.112: 50 0.112 - 0.150: 8 0.150 - 0.187: 4 Chirality restraints: 573 Sorted by residual: chirality pdb=" CA ALA C 67 " pdb=" N ALA C 67 " pdb=" C ALA C 67 " pdb=" CB ALA C 67 " both_signs ideal model delta sigma weight residual False 2.48 2.30 0.19 2.00e-01 2.50e+01 8.74e-01 chirality pdb=" CA ASP C 68 " pdb=" N ASP C 68 " pdb=" C ASP C 68 " pdb=" CB ASP C 68 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.49e-01 chirality pdb=" CA VAL C 20 " pdb=" N VAL C 20 " pdb=" C VAL C 20 " pdb=" CB VAL C 20 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.87e-01 ... (remaining 570 not shown) Planarity restraints: 601 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 87 " -0.017 2.00e-02 2.50e+03 3.35e-02 1.12e+01 pdb=" C LEU C 87 " 0.058 2.00e-02 2.50e+03 pdb=" O LEU C 87 " -0.022 2.00e-02 2.50e+03 pdb=" N ILE C 88 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS B 437 " -0.056 5.00e-02 4.00e+02 7.96e-02 1.01e+01 pdb=" N PRO B 438 " 0.137 5.00e-02 4.00e+02 pdb=" CA PRO B 438 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 438 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 633 " 0.014 2.00e-02 2.50e+03 2.76e-02 7.64e+00 pdb=" C GLN B 633 " -0.048 2.00e-02 2.50e+03 pdb=" O GLN B 633 " 0.018 2.00e-02 2.50e+03 pdb=" N GLY B 634 " 0.016 2.00e-02 2.50e+03 ... (remaining 598 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 238 2.73 - 3.27: 3480 3.27 - 3.81: 5251 3.81 - 4.36: 6732 4.36 - 4.90: 11171 Nonbonded interactions: 26872 Sorted by model distance: nonbonded pdb=" OD2 ASP B 453 " pdb=" OG SER B 478 " model vdw 2.182 3.040 nonbonded pdb=" OE1 GLU B 513 " pdb=" NZ LYS B 538 " model vdw 2.255 3.120 nonbonded pdb=" O SER B 527 " pdb=" OG SER B 527 " model vdw 2.261 3.040 nonbonded pdb=" NZ LYS B 628 " pdb=" OE1 GLU B 629 " model vdw 2.267 3.120 nonbonded pdb=" O ILE B 381 " pdb=" OG SER B 385 " model vdw 2.330 3.040 ... (remaining 26867 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 1.500 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.750 Find NCS groups from input model: 0.010 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: 0.010 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 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 0.107 3585 Z= 0.315 Angle : 1.028 13.733 4819 Z= 0.696 Chirality : 0.046 0.187 573 Planarity : 0.005 0.080 601 Dihedral : 20.840 86.893 1336 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.67 % Allowed : 12.98 % Favored : 86.35 % Rotamer: Outliers : 3.90 % Allowed : 30.24 % Favored : 65.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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 aren not related in a simple way. whole: -4.43 (0.36), residues: 447 helix: -3.05 (0.31), residues: 177 sheet: -2.98 (0.72), residues: 59 loop : -2.73 (0.41), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 686 TYR 0.006 0.001 TYR B 417 PHE 0.011 0.001 PHE C 112 TRP 0.017 0.002 TRP B 692 HIS 0.004 0.001 HIS B 470 Details of bonding type rmsd covalent geometry : bond 0.00509 ( 3584) covalent geometry : angle 1.02840 ( 4817) SS BOND : bond 0.00292 ( 1) SS BOND : angle 0.56178 ( 2) hydrogen bonds : bond 0.20285 ( 92) hydrogen bonds : angle 7.87946 ( 258) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 894 Ramachandran restraints generated. 447 Oldfield, 0 Emsley, 447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 894 Ramachandran restraints generated. 447 Oldfield, 0 Emsley, 447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 49 time to evaluate : 0.117 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 12 residues processed: 62 average time/residue: 0.0634 time to fit residues: 5.0512 Evaluate side-chains 53 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 41 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 370 ARG Chi-restraints excluded: chain B residue 397 ARG Chi-restraints excluded: chain B residue 416 ARG Chi-restraints excluded: chain B residue 494 ARG Chi-restraints excluded: chain B residue 540 ARG Chi-restraints excluded: chain B residue 614 ARG Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 652 ARG Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 44 ARG Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 62 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 0.0970 chunk 22 optimal weight: 0.9990 chunk 37 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: C 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.163640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.141975 restraints weight = 4556.388| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 2.09 r_work: 0.3552 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 3585 Z= 0.145 Angle : 0.685 7.914 4819 Z= 0.385 Chirality : 0.043 0.165 573 Planarity : 0.004 0.038 601 Dihedral : 9.190 57.441 497 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.67 % Allowed : 13.20 % Favored : 86.13 % Rotamer: Outliers : 3.41 % Allowed : 25.85 % Favored : 70.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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 aren not related in a simple way. whole: -4.16 (0.37), residues: 447 helix: -2.80 (0.31), residues: 179 sheet: -2.85 (0.72), residues: 60 loop : -2.58 (0.42), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 686 TYR 0.006 0.001 TYR B 598 PHE 0.026 0.001 PHE B 409 TRP 0.009 0.001 TRP B 692 HIS 0.005 0.001 HIS B 470 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 3584) covalent geometry : angle 0.68438 ( 4817) SS BOND : bond 0.00385 ( 1) SS BOND : angle 1.65842 ( 2) hydrogen bonds : bond 0.03279 ( 92) hydrogen bonds : angle 6.83792 ( 258) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 894 Ramachandran restraints generated. 447 Oldfield, 0 Emsley, 447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 894 Ramachandran restraints generated. 447 Oldfield, 0 Emsley, 447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 47 time to evaluate : 0.083 Fit side-chains revert: symmetry clash REVERT: B 690 MET cc_start: 0.4481 (tpt) cc_final: 0.3723 (mtp) outliers start: 14 outliers final: 9 residues processed: 61 average time/residue: 0.0492 time to fit residues: 3.9723 Evaluate side-chains 50 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 397 ARG Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 507 SER Chi-restraints excluded: chain B residue 548 ARG Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 675 THR Chi-restraints excluded: chain C residue 16 HIS Chi-restraints excluded: chain C residue 44 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 25 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 chunk 43 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 12 optimal weight: 0.5980 chunk 14 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 555 ASN C 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.157552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.135786 restraints weight = 4620.982| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 1.98 r_work: 0.3480 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3585 Z= 0.194 Angle : 0.708 7.850 4819 Z= 0.397 Chirality : 0.045 0.140 573 Planarity : 0.004 0.036 601 Dihedral : 7.442 56.416 461 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.45 % Allowed : 12.98 % Favored : 86.58 % Rotamer: Outliers : 6.59 % Allowed : 25.37 % Favored : 68.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.30 (0.36), residues: 447 helix: -2.88 (0.31), residues: 179 sheet: -2.96 (0.68), residues: 60 loop : -2.69 (0.41), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 682 TYR 0.008 0.002 TYR B 417 PHE 0.020 0.002 PHE B 409 TRP 0.015 0.002 TRP B 692 HIS 0.005 0.001 HIS B 470 Details of bonding type rmsd covalent geometry : bond 0.00441 ( 3584) covalent geometry : angle 0.70636 ( 4817) SS BOND : bond 0.00607 ( 1) SS BOND : angle 2.11790 ( 2) hydrogen bonds : bond 0.04040 ( 92) hydrogen bonds : angle 6.76243 ( 258) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 894 Ramachandran restraints generated. 447 Oldfield, 0 Emsley, 447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 894 Ramachandran restraints generated. 447 Oldfield, 0 Emsley, 447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 42 time to evaluate : 0.087 Fit side-chains revert: symmetry clash REVERT: B 373 VAL cc_start: 0.6760 (OUTLIER) cc_final: 0.6365 (t) REVERT: B 572 ASN cc_start: 0.8628 (OUTLIER) cc_final: 0.8115 (t0) REVERT: B 690 MET cc_start: 0.4983 (tpt) cc_final: 0.3730 (mtp) REVERT: C 82 LYS cc_start: 0.8798 (ttmm) cc_final: 0.8320 (ttmt) REVERT: C 95 LYS cc_start: 0.7838 (ttpt) cc_final: 0.7589 (ttmt) outliers start: 27 outliers final: 19 residues processed: 64 average time/residue: 0.0511 time to fit residues: 4.1684 Evaluate side-chains 59 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 38 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 397 ARG Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 499 GLU Chi-restraints excluded: chain B residue 507 SER Chi-restraints excluded: chain B residue 513 GLU Chi-restraints excluded: chain B residue 548 ARG Chi-restraints excluded: chain B residue 554 ASP Chi-restraints excluded: chain B residue 555 ASN Chi-restraints excluded: chain B residue 572 ASN Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 675 THR Chi-restraints excluded: chain C residue 16 HIS Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 28 ARG Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 93 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 23 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 19 optimal weight: 0.3980 chunk 18 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.162311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.137623 restraints weight = 4579.112| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 1.90 r_work: 0.3514 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3585 Z= 0.133 Angle : 0.629 8.290 4819 Z= 0.355 Chirality : 0.043 0.126 573 Planarity : 0.003 0.036 601 Dihedral : 6.949 53.382 457 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.22 % Allowed : 12.75 % Favored : 87.02 % Rotamer: Outliers : 6.59 % Allowed : 25.61 % Favored : 67.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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 aren not related in a simple way. whole: -4.09 (0.36), residues: 447 helix: -2.63 (0.32), residues: 176 sheet: -2.82 (0.70), residues: 58 loop : -2.67 (0.41), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 682 TYR 0.005 0.001 TYR B 598 PHE 0.006 0.001 PHE B 409 TRP 0.007 0.001 TRP B 692 HIS 0.003 0.001 HIS B 470 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 3584) covalent geometry : angle 0.62850 ( 4817) SS BOND : bond 0.00351 ( 1) SS BOND : angle 1.53038 ( 2) hydrogen bonds : bond 0.03106 ( 92) hydrogen bonds : angle 6.53010 ( 258) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 894 Ramachandran restraints generated. 447 Oldfield, 0 Emsley, 447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 894 Ramachandran restraints generated. 447 Oldfield, 0 Emsley, 447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 44 time to evaluate : 0.157 Fit side-chains REVERT: B 363 LYS cc_start: 0.8249 (mtmt) cc_final: 0.7409 (mtpp) REVERT: B 364 GLN cc_start: 0.7932 (OUTLIER) cc_final: 0.7639 (tp40) REVERT: B 373 VAL cc_start: 0.6588 (OUTLIER) cc_final: 0.6179 (t) REVERT: B 572 ASN cc_start: 0.8621 (OUTLIER) cc_final: 0.8132 (t0) REVERT: B 690 MET cc_start: 0.4866 (tpt) cc_final: 0.3746 (mtp) REVERT: C 82 LYS cc_start: 0.8730 (ttmm) cc_final: 0.8140 (ttmt) outliers start: 27 outliers final: 14 residues processed: 66 average time/residue: 0.0412 time to fit residues: 3.6408 Evaluate side-chains 58 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 41 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 364 GLN Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 397 ARG Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 507 SER Chi-restraints excluded: chain B residue 513 GLU Chi-restraints excluded: chain B residue 548 ARG Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 572 ASN Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 675 THR Chi-restraints excluded: chain C residue 16 HIS Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 93 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 13 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 24 optimal weight: 0.3980 chunk 26 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 35 optimal weight: 0.1980 chunk 23 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.162940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.138037 restraints weight = 4606.367| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 1.89 r_work: 0.3521 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3585 Z= 0.131 Angle : 0.621 9.153 4819 Z= 0.348 Chirality : 0.043 0.138 573 Planarity : 0.003 0.036 601 Dihedral : 6.732 53.662 457 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.22 % Allowed : 12.08 % Favored : 87.70 % Rotamer: Outliers : 5.85 % Allowed : 25.37 % Favored : 68.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.97 (0.36), residues: 447 helix: -2.44 (0.33), residues: 176 sheet: -2.95 (0.67), residues: 60 loop : -2.63 (0.41), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG B 686 TYR 0.005 0.001 TYR C 92 PHE 0.017 0.001 PHE B 409 TRP 0.007 0.001 TRP B 692 HIS 0.003 0.001 HIS B 470 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 3584) covalent geometry : angle 0.62064 ( 4817) SS BOND : bond 0.00323 ( 1) SS BOND : angle 1.42835 ( 2) hydrogen bonds : bond 0.02827 ( 92) hydrogen bonds : angle 6.18255 ( 258) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 894 Ramachandran restraints generated. 447 Oldfield, 0 Emsley, 447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 894 Ramachandran restraints generated. 447 Oldfield, 0 Emsley, 447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 42 time to evaluate : 0.146 Fit side-chains revert: symmetry clash REVERT: B 373 VAL cc_start: 0.6530 (OUTLIER) cc_final: 0.6153 (t) REVERT: B 572 ASN cc_start: 0.8611 (OUTLIER) cc_final: 0.8120 (t0) REVERT: B 690 MET cc_start: 0.5103 (tpt) cc_final: 0.3733 (mtt) outliers start: 24 outliers final: 17 residues processed: 62 average time/residue: 0.0461 time to fit residues: 3.7501 Evaluate side-chains 58 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 39 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 397 ARG Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 507 SER Chi-restraints excluded: chain B residue 513 GLU Chi-restraints excluded: chain B residue 548 ARG Chi-restraints excluded: chain B residue 554 ASP Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 572 ASN Chi-restraints excluded: chain B residue 574 CYS Chi-restraints excluded: chain B residue 583 CYS Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 671 ILE Chi-restraints excluded: chain B residue 675 THR Chi-restraints excluded: chain C residue 16 HIS Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 64 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 4 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.158011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.133241 restraints weight = 4621.847| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 1.87 r_work: 0.3466 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3585 Z= 0.180 Angle : 0.679 9.177 4819 Z= 0.381 Chirality : 0.045 0.130 573 Planarity : 0.003 0.036 601 Dihedral : 7.052 57.379 457 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.22 % Allowed : 13.42 % Favored : 86.35 % Rotamer: Outliers : 7.07 % Allowed : 24.63 % Favored : 68.29 % 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 aren not related in a simple way. whole: -4.02 (0.36), residues: 447 helix: -2.45 (0.33), residues: 175 sheet: -3.16 (0.63), residues: 60 loop : -2.64 (0.42), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 686 TYR 0.007 0.001 TYR B 417 PHE 0.016 0.001 PHE B 409 TRP 0.013 0.002 TRP B 692 HIS 0.004 0.001 HIS B 470 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 3584) covalent geometry : angle 0.67828 ( 4817) SS BOND : bond 0.00555 ( 1) SS BOND : angle 1.94794 ( 2) hydrogen bonds : bond 0.03443 ( 92) hydrogen bonds : angle 6.37953 ( 258) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 894 Ramachandran restraints generated. 447 Oldfield, 0 Emsley, 447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 894 Ramachandran restraints generated. 447 Oldfield, 0 Emsley, 447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 41 time to evaluate : 0.104 Fit side-chains revert: symmetry clash REVERT: B 364 GLN cc_start: 0.8167 (OUTLIER) cc_final: 0.7910 (tp40) REVERT: B 373 VAL cc_start: 0.6674 (OUTLIER) cc_final: 0.6269 (t) REVERT: B 447 ASN cc_start: 0.8900 (m110) cc_final: 0.8663 (m110) REVERT: B 572 ASN cc_start: 0.8647 (OUTLIER) cc_final: 0.8130 (t0) REVERT: B 690 MET cc_start: 0.5303 (tpt) cc_final: 0.3640 (mtt) REVERT: C 78 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.6241 (mp0) REVERT: C 82 LYS cc_start: 0.8808 (ttmm) cc_final: 0.8383 (ttmt) outliers start: 29 outliers final: 16 residues processed: 66 average time/residue: 0.0348 time to fit residues: 3.1235 Evaluate side-chains 57 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 37 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 364 GLN Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 397 ARG Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 499 GLU Chi-restraints excluded: chain B residue 507 SER Chi-restraints excluded: chain B residue 513 GLU Chi-restraints excluded: chain B residue 548 ARG Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 572 ASN Chi-restraints excluded: chain B residue 574 CYS Chi-restraints excluded: chain B residue 638 ILE Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 675 THR Chi-restraints excluded: chain C residue 16 HIS Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 28 ARG Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 78 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 18 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.160771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.138020 restraints weight = 4658.888| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 1.92 r_work: 0.3502 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3377 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3585 Z= 0.141 Angle : 0.629 9.158 4819 Z= 0.354 Chirality : 0.044 0.145 573 Planarity : 0.003 0.035 601 Dihedral : 6.892 59.169 457 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.22 % Allowed : 12.98 % Favored : 86.80 % Rotamer: Outliers : 5.61 % Allowed : 26.83 % Favored : 67.56 % 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 aren not related in a simple way. whole: -3.86 (0.37), residues: 447 helix: -2.29 (0.34), residues: 175 sheet: -3.15 (0.63), residues: 60 loop : -2.53 (0.43), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG B 686 TYR 0.005 0.001 TYR B 598 PHE 0.013 0.001 PHE B 409 TRP 0.009 0.001 TRP B 692 HIS 0.003 0.001 HIS B 470 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 3584) covalent geometry : angle 0.62859 ( 4817) SS BOND : bond 0.00363 ( 1) SS BOND : angle 1.51799 ( 2) hydrogen bonds : bond 0.02871 ( 92) hydrogen bonds : angle 6.22994 ( 258) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 894 Ramachandran restraints generated. 447 Oldfield, 0 Emsley, 447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 894 Ramachandran restraints generated. 447 Oldfield, 0 Emsley, 447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 38 time to evaluate : 0.084 Fit side-chains revert: symmetry clash REVERT: B 364 GLN cc_start: 0.7989 (OUTLIER) cc_final: 0.7736 (tp40) REVERT: B 373 VAL cc_start: 0.6501 (OUTLIER) cc_final: 0.6107 (t) REVERT: B 572 ASN cc_start: 0.8622 (OUTLIER) cc_final: 0.8101 (t0) REVERT: B 690 MET cc_start: 0.5210 (tpt) cc_final: 0.3639 (mtt) REVERT: C 82 LYS cc_start: 0.8760 (ttmm) cc_final: 0.8189 (ttmt) outliers start: 23 outliers final: 18 residues processed: 58 average time/residue: 0.0405 time to fit residues: 3.1189 Evaluate side-chains 60 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 39 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 364 GLN Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 397 ARG Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 507 SER Chi-restraints excluded: chain B residue 513 GLU Chi-restraints excluded: chain B residue 548 ARG Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 572 ASN Chi-restraints excluded: chain B residue 574 CYS Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 638 ILE Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 675 THR Chi-restraints excluded: chain C residue 16 HIS Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 79 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 13 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.160615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.137931 restraints weight = 4592.252| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 1.99 r_work: 0.3493 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3585 Z= 0.141 Angle : 0.625 9.268 4819 Z= 0.351 Chirality : 0.044 0.144 573 Planarity : 0.003 0.036 601 Dihedral : 6.835 61.061 457 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.22 % Allowed : 13.87 % Favored : 85.91 % Rotamer: Outliers : 6.10 % Allowed : 26.10 % Favored : 67.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.79 (0.37), residues: 447 helix: -2.14 (0.35), residues: 176 sheet: -3.18 (0.63), residues: 60 loop : -2.56 (0.43), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG B 686 TYR 0.005 0.001 TYR B 475 PHE 0.011 0.001 PHE B 409 TRP 0.010 0.001 TRP B 692 HIS 0.003 0.001 HIS B 470 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 3584) covalent geometry : angle 0.62471 ( 4817) SS BOND : bond 0.00369 ( 1) SS BOND : angle 1.54348 ( 2) hydrogen bonds : bond 0.02909 ( 92) hydrogen bonds : angle 6.16670 ( 258) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 894 Ramachandran restraints generated. 447 Oldfield, 0 Emsley, 447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 894 Ramachandran restraints generated. 447 Oldfield, 0 Emsley, 447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 40 time to evaluate : 0.087 Fit side-chains revert: symmetry clash REVERT: B 364 GLN cc_start: 0.8001 (OUTLIER) cc_final: 0.7705 (tp40) REVERT: B 373 VAL cc_start: 0.6615 (OUTLIER) cc_final: 0.6209 (t) REVERT: B 572 ASN cc_start: 0.8615 (OUTLIER) cc_final: 0.8093 (t0) REVERT: B 690 MET cc_start: 0.5133 (tpt) cc_final: 0.3587 (mtt) REVERT: C 78 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.6675 (pt0) REVERT: C 82 LYS cc_start: 0.8788 (ttmm) cc_final: 0.8415 (ttmt) outliers start: 25 outliers final: 19 residues processed: 61 average time/residue: 0.0363 time to fit residues: 2.9780 Evaluate side-chains 62 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 39 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 364 GLN Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 397 ARG Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 499 GLU Chi-restraints excluded: chain B residue 507 SER Chi-restraints excluded: chain B residue 513 GLU Chi-restraints excluded: chain B residue 548 ARG Chi-restraints excluded: chain B residue 554 ASP Chi-restraints excluded: chain B residue 572 ASN Chi-restraints excluded: chain B residue 574 CYS Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 638 ILE Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 675 THR Chi-restraints excluded: chain C residue 16 HIS Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 79 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 41 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 448 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.154861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.132284 restraints weight = 4564.773| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 1.90 r_work: 0.3446 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 3585 Z= 0.208 Angle : 0.705 9.342 4819 Z= 0.393 Chirality : 0.047 0.134 573 Planarity : 0.004 0.035 601 Dihedral : 7.283 63.925 457 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.22 % Allowed : 13.65 % Favored : 86.13 % Rotamer: Outliers : 6.34 % Allowed : 25.37 % Favored : 68.29 % 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 aren not related in a simple way. whole: -3.87 (0.38), residues: 447 helix: -2.23 (0.34), residues: 175 sheet: -3.33 (0.62), residues: 60 loop : -2.54 (0.44), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 686 TYR 0.008 0.001 TYR B 475 PHE 0.021 0.002 PHE C 125 TRP 0.016 0.002 TRP B 692 HIS 0.005 0.001 HIS B 470 Details of bonding type rmsd covalent geometry : bond 0.00481 ( 3584) covalent geometry : angle 0.70356 ( 4817) SS BOND : bond 0.00647 ( 1) SS BOND : angle 2.14768 ( 2) hydrogen bonds : bond 0.03689 ( 92) hydrogen bonds : angle 6.34978 ( 258) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 894 Ramachandran restraints generated. 447 Oldfield, 0 Emsley, 447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 894 Ramachandran restraints generated. 447 Oldfield, 0 Emsley, 447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 36 time to evaluate : 0.085 Fit side-chains revert: symmetry clash REVERT: B 364 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7958 (tp40) REVERT: B 373 VAL cc_start: 0.6628 (OUTLIER) cc_final: 0.6188 (t) REVERT: B 447 ASN cc_start: 0.8931 (m110) cc_final: 0.8725 (m110) REVERT: B 572 ASN cc_start: 0.8676 (OUTLIER) cc_final: 0.8123 (t0) REVERT: B 690 MET cc_start: 0.5436 (tpt) cc_final: 0.3668 (mtt) REVERT: C 78 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7182 (pt0) REVERT: C 82 LYS cc_start: 0.8845 (ttmm) cc_final: 0.8417 (ttmt) outliers start: 26 outliers final: 18 residues processed: 60 average time/residue: 0.0416 time to fit residues: 3.3377 Evaluate side-chains 57 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 35 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 364 GLN Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 507 SER Chi-restraints excluded: chain B residue 513 GLU Chi-restraints excluded: chain B residue 548 ARG Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 572 ASN Chi-restraints excluded: chain B residue 574 CYS Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 638 ILE Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 675 THR Chi-restraints excluded: chain C residue 16 HIS Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 28 ARG Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 79 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 30 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 26 optimal weight: 0.3980 chunk 22 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.159095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.134460 restraints weight = 4681.337| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 1.87 r_work: 0.3463 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3585 Z= 0.153 Angle : 0.644 9.225 4819 Z= 0.362 Chirality : 0.044 0.145 573 Planarity : 0.003 0.036 601 Dihedral : 6.449 65.270 453 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.22 % Allowed : 12.98 % Favored : 86.80 % Rotamer: Outliers : 5.37 % Allowed : 26.59 % Favored : 68.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.81 (0.38), residues: 447 helix: -2.12 (0.35), residues: 175 sheet: -3.33 (0.61), residues: 60 loop : -2.57 (0.43), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 686 TYR 0.006 0.001 TYR B 475 PHE 0.013 0.001 PHE C 125 TRP 0.012 0.001 TRP B 692 HIS 0.003 0.001 HIS B 470 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 3584) covalent geometry : angle 0.64317 ( 4817) SS BOND : bond 0.00434 ( 1) SS BOND : angle 1.69351 ( 2) hydrogen bonds : bond 0.03048 ( 92) hydrogen bonds : angle 6.24607 ( 258) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 894 Ramachandran restraints generated. 447 Oldfield, 0 Emsley, 447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 894 Ramachandran restraints generated. 447 Oldfield, 0 Emsley, 447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 39 time to evaluate : 0.090 Fit side-chains revert: symmetry clash REVERT: B 364 GLN cc_start: 0.8051 (OUTLIER) cc_final: 0.7825 (tp40) REVERT: B 373 VAL cc_start: 0.6561 (OUTLIER) cc_final: 0.6214 (t) REVERT: B 572 ASN cc_start: 0.8646 (OUTLIER) cc_final: 0.8099 (t0) REVERT: B 690 MET cc_start: 0.5325 (tpt) cc_final: 0.3663 (mtt) REVERT: C 78 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7230 (pt0) REVERT: C 82 LYS cc_start: 0.8810 (ttmm) cc_final: 0.8402 (ttmt) outliers start: 22 outliers final: 18 residues processed: 58 average time/residue: 0.0391 time to fit residues: 3.0733 Evaluate side-chains 60 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 38 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 364 GLN Chi-restraints excluded: chain B residue 372 GLN Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 507 SER Chi-restraints excluded: chain B residue 513 GLU Chi-restraints excluded: chain B residue 548 ARG Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 572 ASN Chi-restraints excluded: chain B residue 574 CYS Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 638 ILE Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 675 THR Chi-restraints excluded: chain C residue 16 HIS Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 79 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 3 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 37 optimal weight: 0.1980 chunk 12 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.157663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.132751 restraints weight = 4602.265| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 1.91 r_work: 0.3423 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3585 Z= 0.172 Angle : 0.664 9.351 4819 Z= 0.372 Chirality : 0.045 0.139 573 Planarity : 0.003 0.035 601 Dihedral : 6.573 67.092 453 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.22 % Allowed : 13.42 % Favored : 86.35 % Rotamer: Outliers : 5.61 % Allowed : 26.59 % Favored : 67.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.76 (0.38), residues: 447 helix: -2.06 (0.35), residues: 173 sheet: -3.41 (0.60), residues: 60 loop : -2.51 (0.44), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 686 TYR 0.007 0.001 TYR B 475 PHE 0.013 0.001 PHE C 125 TRP 0.014 0.002 TRP B 692 HIS 0.004 0.001 HIS B 470 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 3584) covalent geometry : angle 0.66293 ( 4817) SS BOND : bond 0.00510 ( 1) SS BOND : angle 1.90553 ( 2) hydrogen bonds : bond 0.03305 ( 92) hydrogen bonds : angle 6.27167 ( 258) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 982.59 seconds wall clock time: 17 minutes 29.89 seconds (1049.89 seconds total)