Starting phenix.real_space_refine on Tue Feb 11 11:51:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qkk_18464/02_2025/8qkk_18464.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qkk_18464/02_2025/8qkk_18464.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qkk_18464/02_2025/8qkk_18464.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qkk_18464/02_2025/8qkk_18464.map" model { file = "/net/cci-nas-00/data/ceres_data/8qkk_18464/02_2025/8qkk_18464.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qkk_18464/02_2025/8qkk_18464.cif" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.072 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 26 5.16 5 C 3622 2.51 5 N 922 2.21 5 O 1011 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 5581 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 730, 5581 Classifications: {'peptide': 730} Link IDs: {'PTRANS': 36, 'TRANS': 693} Chain breaks: 1 Time building chain proxies: 4.15, per 1000 atoms: 0.74 Number of scatterers: 5581 At special positions: 0 Unit cell: (69.6, 71.775, 105.125, 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 26 16.00 O 1011 8.00 N 922 7.00 C 3622 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.43 Conformation dependent library (CDL) restraints added in 875.4 milliseconds 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1338 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 3 sheets defined 76.3% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 1 through 12 removed outlier: 4.000A pdb=" N TRP A 5 " --> pdb=" O GLY A 1 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 32 Processing helix chain 'A' and resid 33 through 36 Processing helix chain 'A' and resid 48 through 62 Processing helix chain 'A' and resid 64 through 67 removed outlier: 4.189A pdb=" N SER A 67 " --> pdb=" O ASP A 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 64 through 67' Processing helix chain 'A' and resid 75 through 79 removed outlier: 4.077A pdb=" N ASP A 78 " --> pdb=" O PRO A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 101 Processing helix chain 'A' and resid 112 through 114 No H-bonds generated for 'chain 'A' and resid 112 through 114' Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 143 through 159 Proline residue: A 156 - end of helix Processing helix chain 'A' and resid 160 through 164 Processing helix chain 'A' and resid 171 through 205 removed outlier: 3.845A pdb=" N ILE A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY A 183 " --> pdb=" O THR A 179 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ILE A 194 " --> pdb=" O GLU A 190 " (cutoff:3.500A) Proline residue: A 195 - end of helix Processing helix chain 'A' and resid 208 through 211 Processing helix chain 'A' and resid 212 through 234 Processing helix chain 'A' and resid 241 through 272 removed outlier: 4.091A pdb=" N LEU A 251 " --> pdb=" O THR A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 285 Processing helix chain 'A' and resid 285 through 302 Processing helix chain 'A' and resid 303 through 307 Processing helix chain 'A' and resid 309 through 332 Processing helix chain 'A' and resid 332 through 342 Processing helix chain 'A' and resid 343 through 346 removed outlier: 3.748A pdb=" N ASP A 346 " --> pdb=" O PRO A 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 343 through 346' Processing helix chain 'A' and resid 350 through 356 removed outlier: 4.159A pdb=" N ILE A 356 " --> pdb=" O THR A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 374 removed outlier: 3.691A pdb=" N ARG A 367 " --> pdb=" O GLN A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 400 Processing helix chain 'A' and resid 400 through 416 Proline residue: A 407 - end of helix Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 428 through 432 Processing helix chain 'A' and resid 436 through 449 Processing helix chain 'A' and resid 470 through 484 removed outlier: 3.725A pdb=" N VAL A 484 " --> pdb=" O LYS A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 497 removed outlier: 3.857A pdb=" N LYS A 496 " --> pdb=" O ASP A 493 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N MET A 497 " --> pdb=" O PRO A 494 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 493 through 497' Processing helix chain 'A' and resid 525 through 536 removed outlier: 3.572A pdb=" N ASP A 531 " --> pdb=" O ALA A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 584 Proline residue: A 565 - end of helix Processing helix chain 'A' and resid 587 through 612 Processing helix chain 'A' and resid 629 through 660 removed outlier: 3.829A pdb=" N GLY A 633 " --> pdb=" O ALA A 629 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA A 637 " --> pdb=" O GLY A 633 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ARG A 653 " --> pdb=" O PHE A 649 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N MET A 654 " --> pdb=" O LEU A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 695 removed outlier: 4.910A pdb=" N ARG A 677 " --> pdb=" O ALA A 673 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N LEU A 678 " --> pdb=" O THR A 674 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE A 693 " --> pdb=" O VAL A 689 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE A 695 " --> pdb=" O GLY A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 722 removed outlier: 4.639A pdb=" N ILE A 719 " --> pdb=" O ASP A 715 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ARG A 720 " --> pdb=" O ALA A 716 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE A 722 " --> pdb=" O ILE A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 732 removed outlier: 3.605A pdb=" N ALA A 726 " --> pdb=" O PHE A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 737 Processing sheet with id=AA1, first strand: chain 'A' and resid 109 through 110 Processing sheet with id=AA2, first strand: chain 'A' and resid 424 through 425 Processing sheet with id=AA3, first strand: chain 'A' and resid 499 through 500 404 hydrogen bonds defined for protein. 1158 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.97 Time building geometry restraints manager: 1.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1799 1.34 - 1.46: 1211 1.46 - 1.58: 2636 1.58 - 1.69: 0 1.69 - 1.81: 50 Bond restraints: 5696 Sorted by residual: bond pdb=" N GLY A 1 " pdb=" CA GLY A 1 " ideal model delta sigma weight residual 1.451 1.492 -0.041 1.60e-02 3.91e+03 6.44e+00 bond pdb=" N LEU A 248 " pdb=" CA LEU A 248 " ideal model delta sigma weight residual 1.468 1.458 0.010 1.24e-02 6.50e+03 6.49e-01 bond pdb=" CB LYS A 187 " pdb=" CG LYS A 187 " ideal model delta sigma weight residual 1.520 1.539 -0.019 3.00e-02 1.11e+03 4.16e-01 bond pdb=" CA ILE A 194 " pdb=" CB ILE A 194 " ideal model delta sigma weight residual 1.539 1.536 0.003 5.40e-03 3.43e+04 3.66e-01 bond pdb=" CA TRP A 362 " pdb=" CB TRP A 362 " ideal model delta sigma weight residual 1.530 1.540 -0.010 1.69e-02 3.50e+03 3.62e-01 ... (remaining 5691 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.18: 7511 1.18 - 2.37: 190 2.37 - 3.55: 36 3.55 - 4.73: 15 4.73 - 5.92: 2 Bond angle restraints: 7754 Sorted by residual: angle pdb=" N VAL A 586 " pdb=" CA VAL A 586 " pdb=" C VAL A 586 " ideal model delta sigma weight residual 112.96 110.87 2.09 1.00e+00 1.00e+00 4.37e+00 angle pdb=" C THR A 133 " pdb=" N PHE A 134 " pdb=" CA PHE A 134 " ideal model delta sigma weight residual 121.75 118.99 2.76 1.73e+00 3.34e-01 2.55e+00 angle pdb=" C ASN A 361 " pdb=" N TRP A 362 " pdb=" CA TRP A 362 " ideal model delta sigma weight residual 121.54 124.52 -2.98 1.91e+00 2.74e-01 2.43e+00 angle pdb=" CB LYS A 187 " pdb=" CG LYS A 187 " pdb=" CD LYS A 187 " ideal model delta sigma weight residual 111.30 114.68 -3.38 2.30e+00 1.89e-01 2.16e+00 angle pdb=" C VAL A 302 " pdb=" N PRO A 303 " pdb=" CD PRO A 303 " ideal model delta sigma weight residual 125.00 130.92 -5.92 4.10e+00 5.95e-02 2.08e+00 ... (remaining 7749 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.18: 3063 17.18 - 34.36: 260 34.36 - 51.55: 41 51.55 - 68.73: 13 68.73 - 85.91: 11 Dihedral angle restraints: 3388 sinusoidal: 1309 harmonic: 2079 Sorted by residual: dihedral pdb=" CA THR A 717 " pdb=" C THR A 717 " pdb=" N ILE A 718 " pdb=" CA ILE A 718 " ideal model delta harmonic sigma weight residual 180.00 -163.57 -16.43 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CB GLU A 190 " pdb=" CG GLU A 190 " pdb=" CD GLU A 190 " pdb=" OE1 GLU A 190 " ideal model delta sinusoidal sigma weight residual 0.00 -85.91 85.91 1 3.00e+01 1.11e-03 9.91e+00 dihedral pdb=" CB MET A 701 " pdb=" CG MET A 701 " pdb=" SD MET A 701 " pdb=" CE MET A 701 " ideal model delta sinusoidal sigma weight residual -180.00 -122.31 -57.69 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 3385 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 546 0.025 - 0.049: 223 0.049 - 0.074: 94 0.074 - 0.099: 39 0.099 - 0.123: 24 Chirality restraints: 926 Sorted by residual: chirality pdb=" CA VAL A 460 " pdb=" N VAL A 460 " pdb=" C VAL A 460 " pdb=" CB VAL A 460 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.81e-01 chirality pdb=" CA ILE A 72 " pdb=" N ILE A 72 " pdb=" C ILE A 72 " pdb=" CB ILE A 72 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.74e-01 chirality pdb=" CA VAL A 484 " pdb=" N VAL A 484 " pdb=" C VAL A 484 " pdb=" CB VAL A 484 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.47e-01 ... (remaining 923 not shown) Planarity restraints: 978 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 221 " 0.007 2.00e-02 2.50e+03 1.40e-02 1.96e+00 pdb=" C ALA A 221 " -0.024 2.00e-02 2.50e+03 pdb=" O ALA A 221 " 0.009 2.00e-02 2.50e+03 pdb=" N ILE A 222 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 246 " -0.007 2.00e-02 2.50e+03 1.37e-02 1.87e+00 pdb=" C VAL A 246 " 0.024 2.00e-02 2.50e+03 pdb=" O VAL A 246 " -0.009 2.00e-02 2.50e+03 pdb=" N THR A 247 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 223 " -0.007 2.00e-02 2.50e+03 1.34e-02 1.79e+00 pdb=" C ALA A 223 " 0.023 2.00e-02 2.50e+03 pdb=" O ALA A 223 " -0.009 2.00e-02 2.50e+03 pdb=" N GLY A 224 " -0.008 2.00e-02 2.50e+03 ... (remaining 975 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 93 2.69 - 3.24: 6018 3.24 - 3.79: 9052 3.79 - 4.35: 11642 4.35 - 4.90: 20149 Nonbonded interactions: 46954 Sorted by model distance: nonbonded pdb=" OG1 THR A 127 " pdb=" OD1 ASP A 129 " model vdw 2.132 3.040 nonbonded pdb=" NH1 ARG A 167 " pdb=" OE1 GLN A 444 " model vdw 2.290 3.120 nonbonded pdb=" OG SER A 293 " pdb=" OD1 ASP A 645 " model vdw 2.296 3.040 nonbonded pdb=" O GLN A 473 " pdb=" OD1 ASP A 476 " model vdw 2.309 3.040 nonbonded pdb=" NH2 ARG A 288 " pdb=" O ALA A 582 " model vdw 2.328 3.120 ... (remaining 46949 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.880 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 17.890 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 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:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 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 : 0.002 0.041 5696 Z= 0.147 Angle : 0.493 5.917 7754 Z= 0.257 Chirality : 0.038 0.123 926 Planarity : 0.003 0.027 978 Dihedral : 14.137 85.910 2050 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.34), residues: 726 helix: 1.88 (0.25), residues: 490 sheet: 1.27 (0.85), residues: 41 loop : 0.79 (0.51), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 736 HIS 0.002 0.001 HIS A 68 PHE 0.014 0.001 PHE A 134 TYR 0.009 0.001 TYR A 151 ARG 0.002 0.000 ARG A 367 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.573 Fit side-chains revert: symmetry clash REVERT: A 496 LYS cc_start: 0.8176 (ptpp) cc_final: 0.7894 (ptpp) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.1788 time to fit residues: 21.8139 Evaluate side-chains 79 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 61 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 29 optimal weight: 0.5980 chunk 57 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.4312 r_free = 0.4312 target = 0.213713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.187772 restraints weight = 5671.328| |-----------------------------------------------------------------------------| r_work (start): 0.4019 rms_B_bonded: 1.48 r_work: 0.3858 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3716 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 5696 Z= 0.287 Angle : 0.616 6.878 7754 Z= 0.311 Chirality : 0.044 0.179 926 Planarity : 0.004 0.035 978 Dihedral : 4.034 15.985 774 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.01 % Allowed : 8.40 % Favored : 90.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.32), residues: 726 helix: 1.63 (0.24), residues: 500 sheet: 1.09 (0.87), residues: 41 loop : 0.30 (0.50), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 736 HIS 0.006 0.001 HIS A 37 PHE 0.018 0.002 PHE A 311 TYR 0.010 0.001 TYR A 151 ARG 0.006 0.001 ARG A 281 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 0.661 Fit side-chains revert: symmetry clash REVERT: A 61 TYR cc_start: 0.7621 (m-80) cc_final: 0.6992 (m-80) REVERT: A 167 ARG cc_start: 0.8046 (mmm-85) cc_final: 0.7727 (mtm-85) REVERT: A 567 MET cc_start: 0.8256 (tmm) cc_final: 0.7923 (ttt) outliers start: 6 outliers final: 4 residues processed: 89 average time/residue: 0.1842 time to fit residues: 21.7162 Evaluate side-chains 82 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 78 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 709 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 68 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 53 optimal weight: 0.0010 chunk 57 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 60 optimal weight: 0.3980 chunk 36 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 625 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.215135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.186143 restraints weight = 5666.661| |-----------------------------------------------------------------------------| r_work (start): 0.3999 rms_B_bonded: 1.50 r_work: 0.3856 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3708 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 5696 Z= 0.224 Angle : 0.564 6.801 7754 Z= 0.282 Chirality : 0.041 0.159 926 Planarity : 0.004 0.032 978 Dihedral : 3.953 16.607 774 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.85 % Allowed : 9.75 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.32), residues: 726 helix: 1.61 (0.23), residues: 500 sheet: 0.88 (0.87), residues: 41 loop : 0.23 (0.49), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 736 HIS 0.006 0.001 HIS A 37 PHE 0.017 0.001 PHE A 311 TYR 0.009 0.001 TYR A 151 ARG 0.005 0.000 ARG A 281 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.557 Fit side-chains revert: symmetry clash REVERT: A 167 ARG cc_start: 0.8192 (mmm-85) cc_final: 0.7777 (mtm-85) REVERT: A 496 LYS cc_start: 0.7976 (ptpp) cc_final: 0.7711 (ptpp) REVERT: A 567 MET cc_start: 0.8295 (tmm) cc_final: 0.7896 (ttt) outliers start: 11 outliers final: 5 residues processed: 94 average time/residue: 0.1882 time to fit residues: 22.9407 Evaluate side-chains 83 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 78 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 625 GLN Chi-restraints excluded: chain A residue 636 ILE Chi-restraints excluded: chain A residue 709 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 3 optimal weight: 0.0970 chunk 59 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 55 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 625 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.214044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.182575 restraints weight = 5817.831| |-----------------------------------------------------------------------------| r_work (start): 0.4009 rms_B_bonded: 1.66 r_work: 0.3824 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5696 Z= 0.221 Angle : 0.571 7.799 7754 Z= 0.283 Chirality : 0.042 0.302 926 Planarity : 0.004 0.032 978 Dihedral : 3.981 16.680 774 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.51 % Allowed : 10.76 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.32), residues: 726 helix: 1.62 (0.24), residues: 500 sheet: 0.80 (0.88), residues: 41 loop : 0.16 (0.48), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 736 HIS 0.006 0.001 HIS A 37 PHE 0.017 0.001 PHE A 311 TYR 0.009 0.001 TYR A 151 ARG 0.004 0.000 ARG A 281 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.597 Fit side-chains revert: symmetry clash REVERT: A 167 ARG cc_start: 0.8066 (mmm-85) cc_final: 0.7654 (mtm-85) REVERT: A 496 LYS cc_start: 0.7957 (ptpp) cc_final: 0.7657 (ptpp) REVERT: A 700 MET cc_start: 0.8226 (mtm) cc_final: 0.7956 (mtm) outliers start: 9 outliers final: 4 residues processed: 91 average time/residue: 0.1864 time to fit residues: 22.1237 Evaluate side-chains 83 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 79 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 625 GLN Chi-restraints excluded: chain A residue 709 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 5 optimal weight: 0.8980 chunk 46 optimal weight: 30.0000 chunk 3 optimal weight: 0.2980 chunk 61 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 19 optimal weight: 0.4980 chunk 52 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 = 0.4299 r_free = 0.4299 target = 0.213177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.181649 restraints weight = 5695.203| |-----------------------------------------------------------------------------| r_work (start): 0.3963 rms_B_bonded: 1.65 r_work: 0.3824 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3675 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5696 Z= 0.230 Angle : 0.577 7.123 7754 Z= 0.287 Chirality : 0.042 0.247 926 Planarity : 0.004 0.032 978 Dihedral : 3.999 16.686 774 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.18 % Allowed : 12.61 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.32), residues: 726 helix: 1.59 (0.24), residues: 500 sheet: 0.81 (0.88), residues: 41 loop : 0.16 (0.47), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 736 HIS 0.005 0.001 HIS A 37 PHE 0.017 0.001 PHE A 311 TYR 0.010 0.001 TYR A 646 ARG 0.004 0.000 ARG A 266 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 78 time to evaluate : 0.626 Fit side-chains REVERT: A 167 ARG cc_start: 0.8203 (mmm-85) cc_final: 0.7700 (mtm-85) REVERT: A 496 LYS cc_start: 0.7930 (ptpp) cc_final: 0.7611 (ptpp) REVERT: A 567 MET cc_start: 0.8278 (tmm) cc_final: 0.7650 (ttt) REVERT: A 658 ARG cc_start: 0.7650 (tpp-160) cc_final: 0.7283 (tpt90) outliers start: 7 outliers final: 5 residues processed: 83 average time/residue: 0.2030 time to fit residues: 21.8465 Evaluate side-chains 82 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 77 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLN Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 636 ILE Chi-restraints excluded: chain A residue 709 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 48 optimal weight: 9.9990 chunk 15 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.4280 r_free = 0.4280 target = 0.210720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.178943 restraints weight = 5730.866| |-----------------------------------------------------------------------------| r_work (start): 0.3936 rms_B_bonded: 1.66 r_work: 0.3792 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3645 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5696 Z= 0.266 Angle : 0.612 10.143 7754 Z= 0.302 Chirality : 0.044 0.346 926 Planarity : 0.004 0.032 978 Dihedral : 4.068 16.736 774 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.18 % Allowed : 13.11 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.32), residues: 726 helix: 1.47 (0.23), residues: 499 sheet: 0.68 (0.88), residues: 41 loop : 0.12 (0.47), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 736 HIS 0.005 0.001 HIS A 37 PHE 0.017 0.001 PHE A 311 TYR 0.012 0.001 TYR A 646 ARG 0.004 0.000 ARG A 266 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 0.570 Fit side-chains revert: symmetry clash REVERT: A 167 ARG cc_start: 0.8215 (mmm-85) cc_final: 0.7736 (mtm-85) REVERT: A 567 MET cc_start: 0.8306 (tmm) cc_final: 0.7696 (ttt) REVERT: A 658 ARG cc_start: 0.7688 (tpp-160) cc_final: 0.7350 (tpt90) REVERT: A 700 MET cc_start: 0.8297 (mtm) cc_final: 0.8005 (mtm) outliers start: 7 outliers final: 4 residues processed: 90 average time/residue: 0.2035 time to fit residues: 23.5309 Evaluate side-chains 86 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 82 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLN Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 636 ILE Chi-restraints excluded: chain A residue 709 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 20 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 48 optimal weight: 20.0000 chunk 28 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 24 optimal weight: 0.5980 chunk 70 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 625 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.211440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.179649 restraints weight = 5744.615| |-----------------------------------------------------------------------------| r_work (start): 0.3973 rms_B_bonded: 1.66 r_work: 0.3786 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5696 Z= 0.243 Angle : 0.612 14.262 7754 Z= 0.297 Chirality : 0.043 0.327 926 Planarity : 0.004 0.032 978 Dihedral : 4.051 17.326 774 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.35 % Allowed : 13.45 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.32), residues: 726 helix: 1.48 (0.24), residues: 499 sheet: 0.66 (0.87), residues: 41 loop : 0.13 (0.47), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 736 HIS 0.005 0.001 HIS A 37 PHE 0.017 0.001 PHE A 311 TYR 0.011 0.001 TYR A 646 ARG 0.003 0.000 ARG A 266 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.595 Fit side-chains REVERT: A 167 ARG cc_start: 0.8057 (mmm-85) cc_final: 0.7649 (mtm-85) REVERT: A 567 MET cc_start: 0.8207 (tmm) cc_final: 0.7568 (ttt) REVERT: A 658 ARG cc_start: 0.7804 (tpp-160) cc_final: 0.7474 (tpt90) REVERT: A 700 MET cc_start: 0.8241 (mtm) cc_final: 0.7951 (mtm) outliers start: 14 outliers final: 10 residues processed: 95 average time/residue: 0.2012 time to fit residues: 25.0383 Evaluate side-chains 90 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLN Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 625 GLN Chi-restraints excluded: chain A residue 636 ILE Chi-restraints excluded: chain A residue 709 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 60 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 42 optimal weight: 0.1980 chunk 32 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 29 optimal weight: 0.4980 chunk 9 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.211649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.179772 restraints weight = 5702.177| |-----------------------------------------------------------------------------| r_work (start): 0.3963 rms_B_bonded: 1.64 r_work: 0.3785 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5696 Z= 0.228 Angle : 0.616 14.953 7754 Z= 0.299 Chirality : 0.043 0.295 926 Planarity : 0.004 0.031 978 Dihedral : 4.076 17.387 774 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.02 % Allowed : 13.95 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.32), residues: 726 helix: 1.49 (0.24), residues: 499 sheet: 0.67 (0.88), residues: 41 loop : 0.13 (0.47), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 736 HIS 0.005 0.001 HIS A 37 PHE 0.017 0.001 PHE A 311 TYR 0.012 0.001 TYR A 646 ARG 0.005 0.000 ARG A 167 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.552 Fit side-chains REVERT: A 167 ARG cc_start: 0.8075 (mmm-85) cc_final: 0.7628 (mtm-85) REVERT: A 567 MET cc_start: 0.8209 (tmm) cc_final: 0.7571 (ttt) REVERT: A 700 MET cc_start: 0.8245 (mtm) cc_final: 0.7957 (mtm) outliers start: 12 outliers final: 10 residues processed: 90 average time/residue: 0.1876 time to fit residues: 22.0384 Evaluate side-chains 90 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLN Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 636 ILE Chi-restraints excluded: chain A residue 709 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 44 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4285 r_free = 0.4285 target = 0.211418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.179903 restraints weight = 5726.378| |-----------------------------------------------------------------------------| r_work (start): 0.3959 rms_B_bonded: 1.65 r_work: 0.3779 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5696 Z= 0.239 Angle : 0.622 14.636 7754 Z= 0.301 Chirality : 0.044 0.396 926 Planarity : 0.004 0.031 978 Dihedral : 4.064 17.320 774 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.02 % Allowed : 13.61 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.32), residues: 726 helix: 1.52 (0.24), residues: 493 sheet: 0.61 (0.87), residues: 41 loop : 0.19 (0.46), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 736 HIS 0.005 0.001 HIS A 37 PHE 0.017 0.001 PHE A 311 TYR 0.014 0.001 TYR A 646 ARG 0.003 0.000 ARG A 266 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.585 Fit side-chains REVERT: A 167 ARG cc_start: 0.8105 (mmm-85) cc_final: 0.7784 (mtm-85) REVERT: A 567 MET cc_start: 0.8200 (tmm) cc_final: 0.7581 (ttt) REVERT: A 700 MET cc_start: 0.8262 (mtm) cc_final: 0.7985 (mtm) outliers start: 12 outliers final: 10 residues processed: 90 average time/residue: 0.1891 time to fit residues: 22.1871 Evaluate side-chains 90 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLN Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 367 ARG Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 636 ILE Chi-restraints excluded: chain A residue 709 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 51 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 42 optimal weight: 0.0870 chunk 44 optimal weight: 0.8980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 625 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.212359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.180967 restraints weight = 5784.311| |-----------------------------------------------------------------------------| r_work (start): 0.3952 rms_B_bonded: 1.63 r_work: 0.3815 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3668 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5696 Z= 0.222 Angle : 0.622 14.796 7754 Z= 0.300 Chirality : 0.043 0.402 926 Planarity : 0.004 0.031 978 Dihedral : 4.040 17.330 774 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.35 % Allowed : 13.78 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.32), residues: 726 helix: 1.56 (0.24), residues: 493 sheet: 0.71 (0.88), residues: 41 loop : 0.21 (0.46), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 736 HIS 0.006 0.001 HIS A 37 PHE 0.016 0.001 PHE A 311 TYR 0.013 0.001 TYR A 646 ARG 0.003 0.000 ARG A 266 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.664 Fit side-chains REVERT: A 167 ARG cc_start: 0.8227 (mmm-85) cc_final: 0.7846 (mtm-85) REVERT: A 567 MET cc_start: 0.8345 (tmm) cc_final: 0.7751 (ttt) REVERT: A 700 MET cc_start: 0.8326 (mtm) cc_final: 0.8000 (mtm) outliers start: 14 outliers final: 11 residues processed: 89 average time/residue: 0.1970 time to fit residues: 23.4462 Evaluate side-chains 89 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLN Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 625 GLN Chi-restraints excluded: chain A residue 636 ILE Chi-restraints excluded: chain A residue 709 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 58 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 15 optimal weight: 0.4980 chunk 59 optimal weight: 0.9980 chunk 28 optimal weight: 0.4980 chunk 5 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 12 optimal weight: 6.9990 chunk 50 optimal weight: 0.0970 chunk 32 optimal weight: 0.5980 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 = 0.4292 r_free = 0.4292 target = 0.212050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.180451 restraints weight = 5769.222| |-----------------------------------------------------------------------------| r_work (start): 0.3968 rms_B_bonded: 1.65 r_work: 0.3784 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.141 5696 Z= 0.294 Angle : 1.149 59.189 7754 Z= 0.646 Chirality : 0.046 0.529 926 Planarity : 0.004 0.031 978 Dihedral : 4.038 17.334 774 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.85 % Allowed : 14.29 % Favored : 83.87 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.32), residues: 726 helix: 1.56 (0.24), residues: 493 sheet: 0.70 (0.88), residues: 41 loop : 0.18 (0.46), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 736 HIS 0.005 0.001 HIS A 37 PHE 0.016 0.001 PHE A 311 TYR 0.012 0.001 TYR A 646 ARG 0.002 0.000 ARG A 281 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2980.48 seconds wall clock time: 53 minutes 24.03 seconds (3204.03 seconds total)