Starting phenix.real_space_refine on Fri May 9 19:41:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uah_42064/05_2025/8uah_42064.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uah_42064/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8uah_42064/05_2025/8uah_42064.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uah_42064/05_2025/8uah_42064.map" model { file = "/net/cci-nas-00/data/ceres_data/8uah_42064/05_2025/8uah_42064.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uah_42064/05_2025/8uah_42064.cif" } resolution = 3.3 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= -0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 3.02, per 1000 atoms: 0.85 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: 0.71 Conformation dependent library (CDL) restraints added in 506.8 milliseconds 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: 0.41 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: 0.92 Time building geometry restraints manager: 0.86 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: 1.180 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 13.750 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:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.330 ------------------------------------------------------------------------------- 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 (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: -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 TRP 0.017 0.002 TRP B 692 HIS 0.004 0.001 HIS B 470 PHE 0.011 0.001 PHE C 112 TYR 0.006 0.001 TYR B 417 ARG 0.001 0.000 ARG B 686 Details of bonding type rmsd hydrogen bonds : bond 0.20285 ( 92) hydrogen bonds : angle 7.87946 ( 258) SS BOND : bond 0.00292 ( 1) SS BOND : angle 0.56178 ( 2) covalent geometry : bond 0.00509 ( 3584) covalent geometry : angle 1.02840 ( 4817) *********************** 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 : 0.416 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 12 residues processed: 62 average time/residue: 0.1452 time to fit residues: 11.5321 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 : 0.410 ------------------------------------------------------------------------------- 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 37 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 18 optimal weight: 0.0040 chunk 11 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.163605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.141914 restraints weight = 4571.489| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 2.10 r_work: 0.3546 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3418 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 3585 Z= 0.145 Angle : 0.684 7.887 4819 Z= 0.384 Chirality : 0.043 0.161 573 Planarity : 0.004 0.038 601 Dihedral : 9.210 57.514 497 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.67 % Allowed : 13.20 % Favored : 86.13 % Rotamer: Outliers : 3.41 % Allowed : 26.34 % Favored : 70.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -4.12 (0.37), residues: 447 helix: -2.81 (0.31), residues: 179 sheet: -2.77 (0.74), residues: 58 loop : -2.56 (0.42), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 692 HIS 0.005 0.001 HIS B 470 PHE 0.026 0.001 PHE B 409 TYR 0.006 0.001 TYR B 598 ARG 0.001 0.000 ARG B 686 Details of bonding type rmsd hydrogen bonds : bond 0.03306 ( 92) hydrogen bonds : angle 6.82999 ( 258) SS BOND : bond 0.00346 ( 1) SS BOND : angle 1.63512 ( 2) covalent geometry : bond 0.00310 ( 3584) covalent geometry : angle 0.68371 ( 4817) *********************** 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 : 0.376 Fit side-chains revert: symmetry clash REVERT: B 690 MET cc_start: 0.4507 (tpt) cc_final: 0.3675 (mtp) outliers start: 14 outliers final: 9 residues processed: 61 average time/residue: 0.1311 time to fit residues: 10.4480 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 : 0.394 ------------------------------------------------------------------------------- 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 30 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3919 r_free = 0.3919 target = 0.163046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.140975 restraints weight = 4580.317| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 1.96 r_work: 0.3540 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3412 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1710 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= 0.148 Angle : 0.650 7.932 4819 Z= 0.366 Chirality : 0.043 0.127 573 Planarity : 0.003 0.036 601 Dihedral : 7.080 55.567 461 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.45 % Allowed : 12.53 % Favored : 87.02 % Rotamer: Outliers : 6.10 % Allowed : 25.61 % Favored : 68.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -4.14 (0.36), residues: 447 helix: -2.76 (0.31), residues: 179 sheet: -2.86 (0.70), residues: 58 loop : -2.61 (0.41), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 692 HIS 0.003 0.001 HIS B 470 PHE 0.021 0.001 PHE B 409 TYR 0.005 0.001 TYR B 668 ARG 0.001 0.000 ARG B 682 Details of bonding type rmsd hydrogen bonds : bond 0.03391 ( 92) hydrogen bonds : angle 6.62810 ( 258) SS BOND : bond 0.00399 ( 1) SS BOND : angle 1.62727 ( 2) covalent geometry : bond 0.00318 ( 3584) covalent geometry : angle 0.64890 ( 4817) *********************** 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 66 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 41 time to evaluate : 0.380 Fit side-chains revert: symmetry clash REVERT: B 373 VAL cc_start: 0.6758 (OUTLIER) cc_final: 0.6362 (t) REVERT: B 572 ASN cc_start: 0.8603 (OUTLIER) cc_final: 0.8108 (t0) REVERT: B 690 MET cc_start: 0.4771 (tpt) cc_final: 0.3700 (mtp) outliers start: 25 outliers final: 16 residues processed: 61 average time/residue: 0.1271 time to fit residues: 10.1156 Evaluate side-chains 56 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 38 time to evaluate : 0.388 ------------------------------------------------------------------------------- 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 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 28 ARG 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 15 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 41 optimal weight: 0.0040 chunk 9 optimal weight: 2.9990 chunk 35 optimal weight: 0.0970 chunk 0 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- 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 = 0.3935 r_free = 0.3935 target = 0.164875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.139870 restraints weight = 4541.513| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 1.92 r_work: 0.3533 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3400 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1978 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= 0.126 Angle : 0.617 8.161 4819 Z= 0.347 Chirality : 0.042 0.128 573 Planarity : 0.003 0.035 601 Dihedral : 6.725 54.030 457 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.22 % Allowed : 13.20 % Favored : 86.58 % Rotamer: Outliers : 6.10 % Allowed : 25.37 % Favored : 68.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -4.05 (0.36), residues: 447 helix: -2.55 (0.32), residues: 176 sheet: -2.92 (0.67), residues: 60 loop : -2.66 (0.41), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 692 HIS 0.003 0.001 HIS B 470 PHE 0.020 0.001 PHE B 409 TYR 0.005 0.001 TYR B 598 ARG 0.000 0.000 ARG B 686 Details of bonding type rmsd hydrogen bonds : bond 0.02959 ( 92) hydrogen bonds : angle 6.42100 ( 258) SS BOND : bond 0.00303 ( 1) SS BOND : angle 1.34732 ( 2) covalent geometry : bond 0.00257 ( 3584) covalent geometry : angle 0.61622 ( 4817) *********************** 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 66 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 41 time to evaluate : 0.407 Fit side-chains REVERT: B 363 LYS cc_start: 0.8215 (mtmt) cc_final: 0.7410 (mtpp) REVERT: B 373 VAL cc_start: 0.6581 (OUTLIER) cc_final: 0.6191 (t) REVERT: B 524 MET cc_start: 0.9065 (tmm) cc_final: 0.8830 (tmm) REVERT: B 572 ASN cc_start: 0.8591 (OUTLIER) cc_final: 0.8111 (t0) REVERT: B 690 MET cc_start: 0.4841 (tpt) cc_final: 0.3752 (mtm) outliers start: 25 outliers final: 16 residues processed: 62 average time/residue: 0.1256 time to fit residues: 10.2282 Evaluate side-chains 56 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 38 time to evaluate : 0.405 ------------------------------------------------------------------------------- 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 561 ILE Chi-restraints excluded: chain B residue 572 ASN Chi-restraints excluded: chain B residue 604 ILE 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 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 32 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 20 optimal weight: 0.0060 chunk 3 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 overall best weight: 0.5796 ------------------------------------------------------------------------------- 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 = 0.3942 r_free = 0.3942 target = 0.165514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.142840 restraints weight = 4584.698| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 1.95 r_work: 0.3546 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3407 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2243 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= 0.124 Angle : 0.601 9.029 4819 Z= 0.339 Chirality : 0.043 0.140 573 Planarity : 0.003 0.035 601 Dihedral : 6.548 53.717 457 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.22 % Allowed : 12.08 % Favored : 87.70 % Rotamer: Outliers : 6.34 % Allowed : 24.88 % 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 (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: -3.87 (0.37), residues: 447 helix: -2.32 (0.34), residues: 176 sheet: -2.89 (0.67), residues: 60 loop : -2.60 (0.42), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 692 HIS 0.003 0.001 HIS C 60 PHE 0.017 0.001 PHE B 409 TYR 0.005 0.001 TYR C 92 ARG 0.001 0.000 ARG B 686 Details of bonding type rmsd hydrogen bonds : bond 0.02772 ( 92) hydrogen bonds : angle 6.10012 ( 258) SS BOND : bond 0.00301 ( 1) SS BOND : angle 1.30591 ( 2) covalent geometry : bond 0.00251 ( 3584) covalent geometry : angle 0.60067 ( 4817) *********************** 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: 26 poor density : 40 time to evaluate : 0.416 Fit side-chains REVERT: B 363 LYS cc_start: 0.8214 (mtmt) cc_final: 0.7381 (mtpp) REVERT: B 364 GLN cc_start: 0.7761 (OUTLIER) cc_final: 0.7479 (tp40) REVERT: B 373 VAL cc_start: 0.6437 (OUTLIER) cc_final: 0.6056 (t) REVERT: B 572 ASN cc_start: 0.8596 (OUTLIER) cc_final: 0.8084 (t0) REVERT: B 690 MET cc_start: 0.5039 (tpt) cc_final: 0.3826 (mtm) REVERT: C 82 LYS cc_start: 0.8708 (ttmm) cc_final: 0.8241 (ttmt) outliers start: 26 outliers final: 19 residues processed: 61 average time/residue: 0.1324 time to fit residues: 10.4523 Evaluate side-chains 63 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 41 time to evaluate : 0.409 ------------------------------------------------------------------------------- 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 554 ASP Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 572 ASN Chi-restraints excluded: chain B residue 583 CYS Chi-restraints excluded: chain B residue 604 ILE 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 671 ILE 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 0 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 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 555 ASN ** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.156155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.131202 restraints weight = 4656.990| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 1.94 r_work: 0.3391 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 3585 Z= 0.207 Angle : 0.690 9.031 4819 Z= 0.385 Chirality : 0.046 0.132 573 Planarity : 0.003 0.036 601 Dihedral : 7.091 58.081 457 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.22 % Allowed : 13.65 % Favored : 86.13 % Rotamer: Outliers : 6.59 % Allowed : 24.88 % Favored : 68.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.98 (0.37), residues: 447 helix: -2.36 (0.34), residues: 175 sheet: -3.09 (0.65), residues: 60 loop : -2.67 (0.42), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 692 HIS 0.006 0.001 HIS B 470 PHE 0.014 0.001 PHE B 409 TYR 0.007 0.001 TYR B 417 ARG 0.001 0.000 ARG B 686 Details of bonding type rmsd hydrogen bonds : bond 0.03644 ( 92) hydrogen bonds : angle 6.37169 ( 258) SS BOND : bond 0.00664 ( 1) SS BOND : angle 2.10619 ( 2) covalent geometry : bond 0.00475 ( 3584) covalent geometry : angle 0.68877 ( 4817) *********************** 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 71 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 44 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: B 373 VAL cc_start: 0.6750 (OUTLIER) cc_final: 0.6316 (t) REVERT: B 447 ASN cc_start: 0.8934 (m110) cc_final: 0.8681 (m110) REVERT: B 572 ASN cc_start: 0.8670 (OUTLIER) cc_final: 0.8140 (t0) REVERT: B 690 MET cc_start: 0.5316 (tpt) cc_final: 0.3644 (mtt) REVERT: C 82 LYS cc_start: 0.8884 (ttmm) cc_final: 0.8470 (ttmt) outliers start: 27 outliers final: 19 residues processed: 67 average time/residue: 0.1155 time to fit residues: 10.3848 Evaluate side-chains 61 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 40 time to evaluate : 0.378 ------------------------------------------------------------------------------- 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 561 ILE Chi-restraints excluded: chain B residue 572 ASN Chi-restraints excluded: chain B residue 574 CYS 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 9 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 32 optimal weight: 0.0870 chunk 42 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 overall best weight: 1.0760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 555 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.159462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.136753 restraints weight = 4578.673| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 1.96 r_work: 0.3487 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2580 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= 0.161 Angle : 0.659 9.064 4819 Z= 0.368 Chirality : 0.044 0.132 573 Planarity : 0.003 0.036 601 Dihedral : 7.026 57.952 457 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.22 % Allowed : 12.30 % Favored : 87.47 % Rotamer: Outliers : 6.10 % Allowed : 25.85 % 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 (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: -3.93 (0.36), residues: 447 helix: -2.28 (0.34), residues: 175 sheet: -3.19 (0.63), residues: 60 loop : -2.64 (0.42), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 692 HIS 0.004 0.001 HIS B 470 PHE 0.012 0.001 PHE B 409 TYR 0.005 0.001 TYR B 475 ARG 0.001 0.000 ARG B 686 Details of bonding type rmsd hydrogen bonds : bond 0.03145 ( 92) hydrogen bonds : angle 6.27198 ( 258) SS BOND : bond 0.00484 ( 1) SS BOND : angle 1.78178 ( 2) covalent geometry : bond 0.00359 ( 3584) covalent geometry : angle 0.65784 ( 4817) *********************** 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 64 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 39 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: B 364 GLN cc_start: 0.8054 (OUTLIER) cc_final: 0.7804 (tp40) REVERT: B 373 VAL cc_start: 0.6640 (OUTLIER) cc_final: 0.6220 (t) REVERT: B 447 ASN cc_start: 0.8926 (m110) cc_final: 0.8692 (m110) REVERT: B 555 ASN cc_start: 0.8808 (OUTLIER) cc_final: 0.8522 (m110) REVERT: B 572 ASN cc_start: 0.8631 (OUTLIER) cc_final: 0.8099 (t0) REVERT: B 690 MET cc_start: 0.5312 (tpt) cc_final: 0.3685 (mtt) REVERT: C 82 LYS cc_start: 0.8857 (ttmm) cc_final: 0.8451 (ttmt) outliers start: 25 outliers final: 15 residues processed: 60 average time/residue: 0.1160 time to fit residues: 9.2166 Evaluate side-chains 56 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 37 time to evaluate : 0.568 ------------------------------------------------------------------------------- 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 507 SER Chi-restraints excluded: chain B residue 513 GLU Chi-restraints excluded: chain B residue 548 ARG Chi-restraints excluded: chain B residue 555 ASN 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 4 optimal weight: 0.1980 chunk 32 optimal weight: 6.9990 chunk 9 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 12 optimal weight: 0.4980 chunk 43 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3906 r_free = 0.3906 target = 0.161898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.139188 restraints weight = 4570.018| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 1.96 r_work: 0.3512 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2689 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= 0.130 Angle : 0.616 9.097 4819 Z= 0.347 Chirality : 0.043 0.148 573 Planarity : 0.003 0.035 601 Dihedral : 6.810 57.830 457 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.22 % Allowed : 12.98 % Favored : 86.80 % Rotamer: Outliers : 5.61 % Allowed : 26.10 % 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 (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: -3.76 (0.37), residues: 447 helix: -2.14 (0.34), residues: 176 sheet: -3.14 (0.63), residues: 60 loop : -2.54 (0.43), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 692 HIS 0.002 0.001 HIS B 470 PHE 0.011 0.001 PHE B 409 TYR 0.005 0.001 TYR B 598 ARG 0.000 0.000 ARG B 686 Details of bonding type rmsd hydrogen bonds : bond 0.02735 ( 92) hydrogen bonds : angle 6.13561 ( 258) SS BOND : bond 0.00306 ( 1) SS BOND : angle 1.42427 ( 2) covalent geometry : bond 0.00270 ( 3584) covalent geometry : angle 0.61583 ( 4817) *********************** 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 62 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 39 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: B 364 GLN cc_start: 0.7960 (OUTLIER) cc_final: 0.7693 (tp40) REVERT: B 373 VAL cc_start: 0.6497 (OUTLIER) cc_final: 0.6105 (t) REVERT: B 572 ASN cc_start: 0.8614 (OUTLIER) cc_final: 0.8117 (t0) REVERT: B 690 MET cc_start: 0.5247 (tpt) cc_final: 0.3601 (mtt) REVERT: C 78 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.6702 (pt0) REVERT: C 82 LYS cc_start: 0.8823 (ttmm) cc_final: 0.8401 (ttmt) outliers start: 23 outliers final: 15 residues processed: 58 average time/residue: 0.1192 time to fit residues: 9.1833 Evaluate side-chains 57 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 38 time to evaluate : 0.398 ------------------------------------------------------------------------------- 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 554 ASP 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 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 43 optimal weight: 0.1980 chunk 32 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 30 optimal weight: 0.1980 chunk 29 optimal weight: 0.3980 chunk 38 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 chunk 33 optimal weight: 0.0020 chunk 39 optimal weight: 0.9980 chunk 24 optimal weight: 0.4980 overall best weight: 0.2588 ------------------------------------------------------------------------------- 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 = 0.3968 r_free = 0.3968 target = 0.167788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.145260 restraints weight = 4516.270| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 1.92 r_work: 0.3566 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3437 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 3585 Z= 0.110 Angle : 0.576 9.000 4819 Z= 0.325 Chirality : 0.042 0.155 573 Planarity : 0.003 0.033 601 Dihedral : 6.315 56.633 457 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.22 % Allowed : 11.86 % Favored : 87.92 % Rotamer: Outliers : 3.41 % Allowed : 28.05 % Favored : 68.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.45 (0.38), residues: 447 helix: -1.75 (0.36), residues: 173 sheet: -3.28 (0.65), residues: 55 loop : -2.42 (0.42), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 626 HIS 0.003 0.001 HIS C 60 PHE 0.010 0.001 PHE B 409 TYR 0.007 0.001 TYR B 598 ARG 0.000 0.000 ARG B 682 Details of bonding type rmsd hydrogen bonds : bond 0.02269 ( 92) hydrogen bonds : angle 5.94552 ( 258) SS BOND : bond 0.00055 ( 1) SS BOND : angle 1.01994 ( 2) covalent geometry : bond 0.00207 ( 3584) covalent geometry : angle 0.57619 ( 4817) *********************** 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 61 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 47 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: B 364 GLN cc_start: 0.7709 (OUTLIER) cc_final: 0.7358 (tp40) REVERT: B 373 VAL cc_start: 0.6283 (OUTLIER) cc_final: 0.5920 (t) REVERT: B 468 ASP cc_start: 0.8495 (t0) cc_final: 0.8293 (t0) REVERT: B 477 ILE cc_start: 0.8268 (mm) cc_final: 0.7813 (pt) REVERT: B 572 ASN cc_start: 0.8537 (OUTLIER) cc_final: 0.8072 (t0) REVERT: B 603 LYS cc_start: 0.7289 (ttpp) cc_final: 0.7054 (mmmt) REVERT: B 690 MET cc_start: 0.4973 (tpt) cc_final: 0.3649 (mtm) REVERT: C 78 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.6329 (mp0) REVERT: C 82 LYS cc_start: 0.8697 (ttmm) cc_final: 0.8348 (ttmt) outliers start: 14 outliers final: 7 residues processed: 60 average time/residue: 0.1159 time to fit residues: 9.2862 Evaluate side-chains 56 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.387 ------------------------------------------------------------------------------- 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 507 SER Chi-restraints excluded: chain B residue 513 GLU Chi-restraints excluded: chain B residue 548 ARG Chi-restraints excluded: chain B residue 572 ASN Chi-restraints excluded: chain B residue 638 ILE Chi-restraints excluded: chain B residue 675 THR Chi-restraints excluded: chain C residue 16 HIS Chi-restraints excluded: chain C residue 78 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 27 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 1 optimal weight: 0.0010 chunk 3 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 overall best weight: 0.6786 ------------------------------------------------------------------------------- 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 = 0.3927 r_free = 0.3927 target = 0.163649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.141268 restraints weight = 4516.113| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 1.91 r_work: 0.3536 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3415 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2866 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= 0.127 Angle : 0.593 8.781 4819 Z= 0.333 Chirality : 0.043 0.146 573 Planarity : 0.003 0.035 601 Dihedral : 5.844 56.830 453 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.22 % Allowed : 12.30 % Favored : 87.47 % Rotamer: Outliers : 2.93 % Allowed : 30.00 % Favored : 67.07 % 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: -3.44 (0.38), residues: 447 helix: -1.78 (0.36), residues: 175 sheet: -3.04 (0.63), residues: 60 loop : -2.41 (0.44), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 692 HIS 0.003 0.001 HIS B 470 PHE 0.009 0.001 PHE B 409 TYR 0.006 0.001 TYR B 598 ARG 0.000 0.000 ARG B 686 Details of bonding type rmsd hydrogen bonds : bond 0.02705 ( 92) hydrogen bonds : angle 5.96252 ( 258) SS BOND : bond 0.00277 ( 1) SS BOND : angle 1.39350 ( 2) covalent geometry : bond 0.00264 ( 3584) covalent geometry : angle 0.59246 ( 4817) ********************** 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 55 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 43 time to evaluate : 0.374 Fit side-chains revert: symmetry clash REVERT: B 364 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.7557 (tp40) REVERT: B 373 VAL cc_start: 0.6373 (OUTLIER) cc_final: 0.6007 (t) REVERT: B 468 ASP cc_start: 0.8543 (t0) cc_final: 0.8316 (t0) REVERT: B 572 ASN cc_start: 0.8591 (OUTLIER) cc_final: 0.8054 (t0) REVERT: B 603 LYS cc_start: 0.7247 (ttpp) cc_final: 0.6982 (mmmt) REVERT: B 690 MET cc_start: 0.5163 (tpt) cc_final: 0.3592 (mtt) REVERT: C 78 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.6636 (pt0) REVERT: C 82 LYS cc_start: 0.8768 (ttmm) cc_final: 0.8354 (ttmt) outliers start: 12 outliers final: 8 residues processed: 55 average time/residue: 0.1278 time to fit residues: 9.2059 Evaluate side-chains 54 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 42 time to evaluate : 0.372 ------------------------------------------------------------------------------- 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 507 SER Chi-restraints excluded: chain B residue 513 GLU Chi-restraints excluded: chain B residue 548 ARG Chi-restraints excluded: chain B residue 572 ASN Chi-restraints excluded: chain B residue 638 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 78 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 35 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 39 optimal weight: 0.6980 chunk 42 optimal weight: 0.4980 chunk 34 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3915 r_free = 0.3915 target = 0.162732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.139967 restraints weight = 4624.593| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.07 r_work: 0.3498 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2942 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= 0.135 Angle : 0.625 10.402 4819 Z= 0.351 Chirality : 0.043 0.146 573 Planarity : 0.003 0.035 601 Dihedral : 5.946 57.926 453 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.22 % Allowed : 12.75 % Favored : 87.02 % Rotamer: Outliers : 3.66 % Allowed : 29.27 % Favored : 67.07 % 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: -3.43 (0.38), residues: 447 helix: -1.76 (0.36), residues: 175 sheet: -3.12 (0.63), residues: 60 loop : -2.39 (0.44), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 692 HIS 0.003 0.001 HIS B 470 PHE 0.008 0.001 PHE B 409 TYR 0.006 0.001 TYR B 598 ARG 0.000 0.000 ARG B 686 Details of bonding type rmsd hydrogen bonds : bond 0.02761 ( 92) hydrogen bonds : angle 5.98602 ( 258) SS BOND : bond 0.00316 ( 1) SS BOND : angle 1.39234 ( 2) covalent geometry : bond 0.00288 ( 3584) covalent geometry : angle 0.62493 ( 4817) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2237.30 seconds wall clock time: 39 minutes 19.40 seconds (2359.40 seconds total)