Starting phenix.real_space_refine on Tue Feb 11 17:31:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a9b_15275/02_2025/8a9b_15275.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a9b_15275/02_2025/8a9b_15275.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8a9b_15275/02_2025/8a9b_15275.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a9b_15275/02_2025/8a9b_15275.map" model { file = "/net/cci-nas-00/data/ceres_data/8a9b_15275/02_2025/8a9b_15275.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a9b_15275/02_2025/8a9b_15275.cif" } resolution = 4.0 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= 0.093 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 8 5.16 5 C 4120 2.51 5 N 1027 2.21 5 O 1231 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-5592/modules/chem_data/mon_lib" Total number of atoms: 6386 Number of models: 1 Model: "" Number of chains: 1 Chain: "B" Number of atoms: 6386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 809, 6386 Classifications: {'peptide': 809} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 786} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Time building chain proxies: 4.05, per 1000 atoms: 0.63 Number of scatterers: 6386 At special positions: 0 Unit cell: (91.41, 103.044, 149.58, 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 8 16.00 O 1231 8.00 N 1027 7.00 C 4120 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: 1.61 Conformation dependent library (CDL) restraints added in 921.4 milliseconds 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1530 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 6 sheets defined 42.3% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'B' and resid 95 through 106 removed outlier: 3.572A pdb=" N GLY B 99 " --> pdb=" O ASP B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 125 removed outlier: 3.820A pdb=" N ALA B 113 " --> pdb=" O LYS B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 256 removed outlier: 3.742A pdb=" N ASN B 255 " --> pdb=" O GLU B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 266 Processing helix chain 'B' and resid 268 through 297 removed outlier: 3.936A pdb=" N GLY B 295 " --> pdb=" O ALA B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 304 removed outlier: 4.202A pdb=" N GLN B 304 " --> pdb=" O GLU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 316 Processing helix chain 'B' and resid 319 through 331 Processing helix chain 'B' and resid 334 through 344 Processing helix chain 'B' and resid 353 through 360 removed outlier: 3.966A pdb=" N LEU B 357 " --> pdb=" O THR B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 370 Processing helix chain 'B' and resid 376 through 381 Processing helix chain 'B' and resid 383 through 389 Processing helix chain 'B' and resid 396 through 414 removed outlier: 4.462A pdb=" N ASP B 406 " --> pdb=" O GLN B 402 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N LEU B 407 " --> pdb=" O SER B 403 " (cutoff:3.500A) Proline residue: B 410 - end of helix Processing helix chain 'B' and resid 421 through 431 removed outlier: 3.647A pdb=" N GLN B 431 " --> pdb=" O GLU B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 462 Processing helix chain 'B' and resid 465 through 477 removed outlier: 4.038A pdb=" N VAL B 469 " --> pdb=" O MET B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 486 Processing helix chain 'B' and resid 489 through 499 Processing helix chain 'B' and resid 515 through 525 Processing helix chain 'B' and resid 532 through 539 Processing helix chain 'B' and resid 552 through 557 removed outlier: 3.647A pdb=" N ALA B 557 " --> pdb=" O ALA B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 582 removed outlier: 3.879A pdb=" N GLU B 569 " --> pdb=" O ASP B 565 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN B 570 " --> pdb=" O TYR B 566 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA B 573 " --> pdb=" O GLU B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 592 Processing helix chain 'B' and resid 635 through 643 Processing helix chain 'B' and resid 649 through 659 removed outlier: 4.131A pdb=" N THR B 653 " --> pdb=" O ASP B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 663 through 674 Processing helix chain 'B' and resid 685 through 689 Processing helix chain 'B' and resid 692 through 700 Processing helix chain 'B' and resid 706 through 717 Processing helix chain 'B' and resid 797 through 816 Processing sheet with id=AA1, first strand: chain 'B' and resid 135 through 137 removed outlier: 4.353A pdb=" N PHE B 157 " --> pdb=" O TYR B 187 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N TYR B 187 " --> pdb=" O PHE B 157 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 141 through 142 removed outlier: 3.618A pdb=" N ASN B 142 " --> pdb=" O ASP B 154 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ASP B 154 " --> pdb=" O ASN B 142 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 189 through 190 removed outlier: 3.584A pdb=" N ASN B 190 " --> pdb=" O THR B 218 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 607 through 609 removed outlier: 3.987A pdb=" N LEU B 614 " --> pdb=" O VAL B 747 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LYS B 618 " --> pdb=" O GLU B 743 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLU B 743 " --> pdb=" O LYS B 618 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ASP B 620 " --> pdb=" O GLY B 741 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N GLY B 741 " --> pdb=" O ASP B 620 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE B 736 " --> pdb=" O VAL B 625 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 607 through 609 removed outlier: 3.987A pdb=" N LEU B 614 " --> pdb=" O VAL B 747 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LYS B 618 " --> pdb=" O GLU B 743 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLU B 743 " --> pdb=" O LYS B 618 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ASP B 620 " --> pdb=" O GLY B 741 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N GLY B 741 " --> pdb=" O ASP B 620 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR B 769 " --> pdb=" O LYS B 739 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N GLU B 743 " --> pdb=" O GLY B 765 " (cutoff:3.500A) removed outlier: 8.570A pdb=" N GLY B 765 " --> pdb=" O GLU B 743 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N LEU B 745 " --> pdb=" O ILE B 763 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N ILE B 763 " --> pdb=" O LEU B 745 " (cutoff:3.500A) removed outlier: 8.664A pdb=" N VAL B 747 " --> pdb=" O TYR B 761 " (cutoff:3.500A) removed outlier: 8.741A pdb=" N TYR B 761 " --> pdb=" O VAL B 747 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N GLN B 762 " --> pdb=" O VAL B 829 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N VAL B 829 " --> pdb=" O GLN B 762 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N ILE B 764 " --> pdb=" O ILE B 827 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N ILE B 827 " --> pdb=" O ILE B 764 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 630 through 632 removed outlier: 3.843A pdb=" N PHE B 630 " --> pdb=" O LEU B 732 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU B 778 " --> pdb=" O THR B 731 " (cutoff:3.500A) 239 hydrogen bonds defined for protein. 687 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: 1.85 Time building geometry restraints manager: 1.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2007 1.34 - 1.45: 795 1.45 - 1.57: 3677 1.57 - 1.69: 0 1.69 - 1.80: 16 Bond restraints: 6495 Sorted by residual: bond pdb=" CA THR B 414 " pdb=" C THR B 414 " ideal model delta sigma weight residual 1.524 1.557 -0.033 1.59e-02 3.96e+03 4.39e+00 bond pdb=" CG1 ILE B 289 " pdb=" CD1 ILE B 289 " ideal model delta sigma weight residual 1.513 1.450 0.063 3.90e-02 6.57e+02 2.65e+00 bond pdb=" CG LEU B 797 " pdb=" CD1 LEU B 797 " ideal model delta sigma weight residual 1.521 1.473 0.048 3.30e-02 9.18e+02 2.10e+00 bond pdb=" CB PRO B 375 " pdb=" CG PRO B 375 " ideal model delta sigma weight residual 1.506 1.458 0.048 3.90e-02 6.57e+02 1.54e+00 bond pdb=" CG PRO B 375 " pdb=" CD PRO B 375 " ideal model delta sigma weight residual 1.512 1.479 0.033 2.70e-02 1.37e+03 1.45e+00 ... (remaining 6490 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.81: 8685 3.81 - 7.62: 56 7.62 - 11.44: 7 11.44 - 15.25: 0 15.25 - 19.06: 2 Bond angle restraints: 8750 Sorted by residual: angle pdb=" C ILE B 374 " pdb=" N PRO B 375 " pdb=" CD PRO B 375 " ideal model delta sigma weight residual 120.60 101.54 19.06 2.20e+00 2.07e-01 7.51e+01 angle pdb=" N PRO B 61 " pdb=" CA PRO B 61 " pdb=" CB PRO B 61 " ideal model delta sigma weight residual 103.25 111.43 -8.18 1.05e+00 9.07e-01 6.07e+01 angle pdb=" C ILE B 374 " pdb=" N PRO B 375 " pdb=" CA PRO B 375 " ideal model delta sigma weight residual 127.00 144.95 -17.95 2.40e+00 1.74e-01 5.59e+01 angle pdb=" C ILE B 374 " pdb=" CA ILE B 374 " pdb=" CB ILE B 374 " ideal model delta sigma weight residual 111.36 120.22 -8.86 1.82e+00 3.02e-01 2.37e+01 angle pdb=" C PHE B 437 " pdb=" N ASP B 438 " pdb=" CA ASP B 438 " ideal model delta sigma weight residual 121.54 129.80 -8.26 1.91e+00 2.74e-01 1.87e+01 ... (remaining 8745 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.67: 3475 16.67 - 33.35: 373 33.35 - 50.02: 79 50.02 - 66.70: 8 66.70 - 83.37: 12 Dihedral angle restraints: 3947 sinusoidal: 1589 harmonic: 2358 Sorted by residual: dihedral pdb=" CA ILE B 374 " pdb=" C ILE B 374 " pdb=" N PRO B 375 " pdb=" CA PRO B 375 " ideal model delta harmonic sigma weight residual 0.00 -34.11 34.11 0 5.00e+00 4.00e-02 4.65e+01 dihedral pdb=" CA ILE B 632 " pdb=" C ILE B 632 " pdb=" N LYS B 633 " pdb=" CA LYS B 633 " ideal model delta harmonic sigma weight residual -180.00 -148.44 -31.56 0 5.00e+00 4.00e-02 3.98e+01 dihedral pdb=" CA GLU B 416 " pdb=" C GLU B 416 " pdb=" N LYS B 417 " pdb=" CA LYS B 417 " ideal model delta harmonic sigma weight residual 180.00 153.22 26.78 0 5.00e+00 4.00e-02 2.87e+01 ... (remaining 3944 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 937 0.096 - 0.191: 57 0.191 - 0.287: 4 0.287 - 0.383: 0 0.383 - 0.478: 1 Chirality restraints: 999 Sorted by residual: chirality pdb=" CB ILE B 374 " pdb=" CA ILE B 374 " pdb=" CG1 ILE B 374 " pdb=" CG2 ILE B 374 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.48 2.00e-01 2.50e+01 5.72e+00 chirality pdb=" CB ILE B 289 " pdb=" CA ILE B 289 " pdb=" CG1 ILE B 289 " pdb=" CG2 ILE B 289 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CB THR B 610 " pdb=" CA THR B 610 " pdb=" OG1 THR B 610 " pdb=" CG2 THR B 610 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 996 not shown) Planarity restraints: 1119 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 686 " 0.044 5.00e-02 4.00e+02 6.76e-02 7.32e+00 pdb=" N PRO B 687 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO B 687 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 687 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 374 " 0.038 5.00e-02 4.00e+02 5.56e-02 4.95e+00 pdb=" N PRO B 375 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO B 375 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 375 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 852 " 0.029 5.00e-02 4.00e+02 4.43e-02 3.14e+00 pdb=" N PRO B 853 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 853 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 853 " 0.025 5.00e-02 4.00e+02 ... (remaining 1116 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 168 2.67 - 3.23: 6610 3.23 - 3.79: 9933 3.79 - 4.34: 13463 4.34 - 4.90: 20822 Nonbonded interactions: 50996 Sorted by model distance: nonbonded pdb=" O ALA B 470 " pdb=" OG1 THR B 473 " model vdw 2.113 3.040 nonbonded pdb=" OG SER B 311 " pdb=" O LEU B 484 " model vdw 2.153 3.040 nonbonded pdb=" OE1 GLU B 306 " pdb=" NZ LYS B 575 " model vdw 2.190 3.120 nonbonded pdb=" OE1 GLU B 758 " pdb=" OG SER B 838 " model vdw 2.211 3.040 nonbonded pdb=" OG1 THR B 768 " pdb=" O PHE B 823 " model vdw 2.220 3.040 ... (remaining 50991 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 group one per residue 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: 1.260 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: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 18.190 Find NCS groups from input model: 0.060 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: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5803 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 : 0.004 0.063 6495 Z= 0.276 Angle : 0.877 19.061 8750 Z= 0.459 Chirality : 0.051 0.478 999 Planarity : 0.005 0.068 1119 Dihedral : 14.890 83.373 2417 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 20.52 Ramachandran Plot: Outliers : 1.00 % Allowed : 14.82 % Favored : 84.18 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.13 % 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: -3.17 (0.28), residues: 803 helix: -0.88 (0.28), residues: 328 sheet: -2.16 (0.78), residues: 50 loop : -3.23 (0.27), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 805 HIS 0.003 0.001 HIS B 216 PHE 0.023 0.002 PHE B 578 TYR 0.029 0.002 TYR B 740 ARG 0.007 0.001 ARG B 140 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 294 MET cc_start: 0.5566 (mtt) cc_final: 0.5230 (mmp) REVERT: B 447 LEU cc_start: 0.7382 (mm) cc_final: 0.7135 (mm) REVERT: B 633 LYS cc_start: 0.8057 (tptm) cc_final: 0.7845 (tptp) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.2002 time to fit residues: 19.9005 Evaluate side-chains 46 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 33 optimal weight: 9.9990 chunk 20 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 62 optimal weight: 0.0020 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 46 optimal weight: 0.3980 chunk 72 optimal weight: 0.4980 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4712 r_free = 0.4712 target = 0.181858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.152098 restraints weight = 17364.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.152996 restraints weight = 13574.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.152886 restraints weight = 12428.779| |-----------------------------------------------------------------------------| r_work (final): 0.4296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6218 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6495 Z= 0.207 Angle : 0.766 10.383 8750 Z= 0.396 Chirality : 0.048 0.508 999 Planarity : 0.004 0.052 1119 Dihedral : 6.166 35.651 838 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 17.09 Ramachandran Plot: Outliers : 0.87 % Allowed : 13.57 % Favored : 85.55 % Rotamer: Outliers : 0.86 % Allowed : 8.86 % Favored : 90.29 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % 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: -3.09 (0.28), residues: 803 helix: -0.98 (0.27), residues: 336 sheet: -2.46 (0.78), residues: 49 loop : -3.01 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 121 HIS 0.002 0.001 HIS B 266 PHE 0.028 0.002 PHE B 854 TYR 0.018 0.001 TYR B 187 ARG 0.002 0.001 ARG B 331 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 183 GLN cc_start: 0.1414 (tm-30) cc_final: 0.1185 (tm-30) REVERT: B 294 MET cc_start: 0.6464 (mtt) cc_final: 0.5683 (mmp) REVERT: B 640 MET cc_start: 0.7830 (ptm) cc_final: 0.7350 (ptm) outliers start: 6 outliers final: 2 residues processed: 63 average time/residue: 0.1679 time to fit residues: 15.0133 Evaluate side-chains 51 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 785 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 3 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 72 optimal weight: 0.3980 chunk 62 optimal weight: 0.0970 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 GLN ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 849 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4674 r_free = 0.4674 target = 0.178535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.150002 restraints weight = 18078.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.149922 restraints weight = 14522.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.149949 restraints weight = 11827.277| |-----------------------------------------------------------------------------| r_work (final): 0.4262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6293 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6495 Z= 0.267 Angle : 0.806 10.005 8750 Z= 0.413 Chirality : 0.048 0.494 999 Planarity : 0.004 0.057 1119 Dihedral : 6.418 35.746 838 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 18.10 Ramachandran Plot: Outliers : 0.75 % Allowed : 13.57 % Favored : 85.68 % Rotamer: Outliers : 1.71 % Allowed : 14.00 % Favored : 84.29 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.13 % 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: -3.16 (0.28), residues: 803 helix: -0.93 (0.28), residues: 330 sheet: -2.74 (0.75), residues: 51 loop : -3.09 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 121 HIS 0.002 0.001 HIS B 266 PHE 0.026 0.002 PHE B 854 TYR 0.016 0.002 TYR B 187 ARG 0.003 0.001 ARG B 708 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.756 Fit side-chains revert: symmetry clash REVERT: B 294 MET cc_start: 0.6411 (mtt) cc_final: 0.6026 (mmp) REVERT: B 640 MET cc_start: 0.8170 (ptm) cc_final: 0.7656 (ptm) outliers start: 12 outliers final: 7 residues processed: 61 average time/residue: 0.1624 time to fit residues: 14.4477 Evaluate side-chains 51 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 465 MET Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 766 VAL Chi-restraints excluded: chain B residue 785 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 60 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 72 optimal weight: 0.3980 chunk 41 optimal weight: 6.9990 chunk 61 optimal weight: 0.8980 chunk 1 optimal weight: 9.9990 chunk 51 optimal weight: 0.5980 chunk 49 optimal weight: 3.9990 chunk 50 optimal weight: 0.0870 chunk 2 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4696 r_free = 0.4696 target = 0.180394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.152856 restraints weight = 18385.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.152474 restraints weight = 14483.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.152535 restraints weight = 12128.229| |-----------------------------------------------------------------------------| r_work (final): 0.4301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6214 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6495 Z= 0.197 Angle : 0.739 12.389 8750 Z= 0.373 Chirality : 0.045 0.255 999 Planarity : 0.004 0.061 1119 Dihedral : 5.979 26.909 838 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.62 % Allowed : 12.83 % Favored : 86.55 % Rotamer: Outliers : 1.57 % Allowed : 17.29 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -2.98 (0.28), residues: 803 helix: -0.74 (0.28), residues: 326 sheet: -2.73 (0.74), residues: 51 loop : -3.00 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 805 HIS 0.002 0.001 HIS B 216 PHE 0.036 0.002 PHE B 111 TYR 0.012 0.001 TYR B 187 ARG 0.005 0.001 ARG B 850 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 183 GLN cc_start: -0.0530 (tm-30) cc_final: -0.0871 (tm-30) REVERT: B 357 LEU cc_start: 0.8605 (tt) cc_final: 0.8338 (tp) REVERT: B 669 ASP cc_start: 0.7243 (m-30) cc_final: 0.6523 (p0) outliers start: 11 outliers final: 9 residues processed: 61 average time/residue: 0.1507 time to fit residues: 13.6399 Evaluate side-chains 51 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 111 PHE Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 465 MET Chi-restraints excluded: chain B residue 474 GLU Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 766 VAL Chi-restraints excluded: chain B residue 785 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 62 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 71 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 863 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4628 r_free = 0.4628 target = 0.174563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.143290 restraints weight = 18183.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.144711 restraints weight = 15401.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.145177 restraints weight = 12551.733| |-----------------------------------------------------------------------------| r_work (final): 0.4216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6442 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 6495 Z= 0.334 Angle : 0.822 9.953 8750 Z= 0.421 Chirality : 0.048 0.244 999 Planarity : 0.005 0.065 1119 Dihedral : 6.403 27.305 838 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 21.38 Ramachandran Plot: Outliers : 0.62 % Allowed : 15.07 % Favored : 84.31 % Rotamer: Outliers : 3.00 % Allowed : 18.14 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -3.34 (0.27), residues: 803 helix: -1.11 (0.27), residues: 332 sheet: -2.71 (0.85), residues: 33 loop : -3.21 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 121 HIS 0.004 0.001 HIS B 216 PHE 0.038 0.002 PHE B 111 TYR 0.015 0.002 TYR B 751 ARG 0.003 0.001 ARG B 708 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 53 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 294 MET cc_start: 0.6592 (mtt) cc_final: 0.6191 (mmp) REVERT: B 447 LEU cc_start: 0.7777 (mm) cc_final: 0.7306 (tp) REVERT: B 483 ASP cc_start: 0.6255 (t0) cc_final: 0.5924 (t0) REVERT: B 579 LYS cc_start: 0.7164 (ptmt) cc_final: 0.6947 (pttp) REVERT: B 640 MET cc_start: 0.8041 (ptp) cc_final: 0.7810 (ptm) REVERT: B 669 ASP cc_start: 0.7721 (m-30) cc_final: 0.6943 (p0) outliers start: 21 outliers final: 14 residues processed: 69 average time/residue: 0.1539 time to fit residues: 15.5926 Evaluate side-chains 61 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 47 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 111 PHE Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 465 MET Chi-restraints excluded: chain B residue 474 GLU Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 649 ASP Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 766 VAL Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 785 LYS Chi-restraints excluded: chain B residue 851 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 4 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 29 optimal weight: 0.0970 chunk 28 optimal weight: 0.6980 chunk 19 optimal weight: 0.0670 chunk 72 optimal weight: 0.4980 chunk 77 optimal weight: 0.0070 chunk 10 optimal weight: 6.9990 chunk 53 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 overall best weight: 0.2734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4688 r_free = 0.4688 target = 0.179809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.153094 restraints weight = 18157.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.153491 restraints weight = 14248.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.152897 restraints weight = 11913.151| |-----------------------------------------------------------------------------| r_work (final): 0.4306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6210 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6495 Z= 0.175 Angle : 0.709 9.982 8750 Z= 0.357 Chirality : 0.044 0.225 999 Planarity : 0.004 0.066 1119 Dihedral : 5.953 25.130 838 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.62 % Allowed : 12.70 % Favored : 86.67 % Rotamer: Outliers : 2.86 % Allowed : 20.57 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -2.97 (0.28), residues: 803 helix: -0.78 (0.28), residues: 328 sheet: -2.10 (0.97), residues: 31 loop : -3.04 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 805 HIS 0.001 0.000 HIS B 216 PHE 0.035 0.002 PHE B 111 TYR 0.013 0.001 TYR B 623 ARG 0.001 0.000 ARG B 140 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 52 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 280 ILE cc_start: 0.6975 (mt) cc_final: 0.6700 (mt) REVERT: B 483 ASP cc_start: 0.6273 (t0) cc_final: 0.5903 (t70) REVERT: B 640 MET cc_start: 0.8032 (ptp) cc_final: 0.7439 (ptm) outliers start: 20 outliers final: 14 residues processed: 69 average time/residue: 0.1477 time to fit residues: 15.1843 Evaluate side-chains 58 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 44 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 111 PHE Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 465 MET Chi-restraints excluded: chain B residue 474 GLU Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 631 GLU Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 766 VAL Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 785 LYS Chi-restraints excluded: chain B residue 817 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 1 optimal weight: 9.9990 chunk 67 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 64 optimal weight: 0.1980 chunk 48 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4659 r_free = 0.4659 target = 0.177262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.147121 restraints weight = 18079.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.148878 restraints weight = 14816.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.149149 restraints weight = 11283.313| |-----------------------------------------------------------------------------| r_work (final): 0.4250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6322 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6495 Z= 0.224 Angle : 0.756 11.124 8750 Z= 0.378 Chirality : 0.046 0.225 999 Planarity : 0.005 0.067 1119 Dihedral : 5.978 24.130 838 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 17.32 Ramachandran Plot: Outliers : 0.62 % Allowed : 14.57 % Favored : 84.81 % Rotamer: Outliers : 2.86 % Allowed : 21.43 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -2.97 (0.28), residues: 803 helix: -0.80 (0.28), residues: 327 sheet: -2.13 (0.96), residues: 32 loop : -3.02 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 121 HIS 0.002 0.001 HIS B 216 PHE 0.040 0.002 PHE B 454 TYR 0.018 0.001 TYR B 206 ARG 0.003 0.001 ARG B 850 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 47 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 183 GLN cc_start: 0.1756 (tm-30) cc_final: 0.1271 (tm-30) REVERT: B 280 ILE cc_start: 0.6987 (mt) cc_final: 0.6634 (mt) REVERT: B 414 THR cc_start: 0.6537 (OUTLIER) cc_final: 0.6196 (p) REVERT: B 483 ASP cc_start: 0.6405 (t0) cc_final: 0.6006 (t70) REVERT: B 740 TYR cc_start: 0.7899 (OUTLIER) cc_final: 0.7322 (t80) outliers start: 20 outliers final: 16 residues processed: 65 average time/residue: 0.1503 time to fit residues: 14.5010 Evaluate side-chains 64 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 46 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 111 PHE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 216 HIS Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 465 MET Chi-restraints excluded: chain B residue 474 GLU Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 631 GLU Chi-restraints excluded: chain B residue 740 TYR Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 766 VAL Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 785 LYS Chi-restraints excluded: chain B residue 817 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 21 optimal weight: 0.6980 chunk 10 optimal weight: 9.9990 chunk 22 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 68 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4650 r_free = 0.4650 target = 0.176361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.145707 restraints weight = 17912.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.147702 restraints weight = 14683.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.148099 restraints weight = 11856.324| |-----------------------------------------------------------------------------| r_work (final): 0.4229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6379 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6495 Z= 0.235 Angle : 0.770 13.365 8750 Z= 0.382 Chirality : 0.046 0.238 999 Planarity : 0.005 0.066 1119 Dihedral : 6.062 23.411 838 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 17.79 Ramachandran Plot: Outliers : 0.50 % Allowed : 14.94 % Favored : 84.56 % Rotamer: Outliers : 3.29 % Allowed : 21.29 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -3.04 (0.28), residues: 803 helix: -0.83 (0.28), residues: 327 sheet: -2.11 (0.94), residues: 32 loop : -3.08 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 121 HIS 0.003 0.001 HIS B 443 PHE 0.036 0.002 PHE B 111 TYR 0.016 0.001 TYR B 206 ARG 0.002 0.000 ARG B 708 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 48 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 280 ILE cc_start: 0.7091 (mt) cc_final: 0.6754 (mt) REVERT: B 414 THR cc_start: 0.6270 (OUTLIER) cc_final: 0.6007 (p) REVERT: B 483 ASP cc_start: 0.6930 (t0) cc_final: 0.6382 (t70) REVERT: B 579 LYS cc_start: 0.7044 (ptmt) cc_final: 0.6838 (pttp) REVERT: B 633 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.7964 (mmmt) REVERT: B 650 LEU cc_start: 0.7339 (OUTLIER) cc_final: 0.7009 (tp) REVERT: B 740 TYR cc_start: 0.7930 (OUTLIER) cc_final: 0.7279 (t80) outliers start: 23 outliers final: 15 residues processed: 68 average time/residue: 0.1526 time to fit residues: 15.0639 Evaluate side-chains 66 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 47 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 111 PHE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 216 HIS Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 474 GLU Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 631 GLU Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 740 TYR Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 766 VAL Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 785 LYS Chi-restraints excluded: chain B residue 817 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 57 optimal weight: 0.1980 chunk 56 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 9 optimal weight: 0.0370 chunk 67 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 2 optimal weight: 0.4980 chunk 45 optimal weight: 0.9990 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4667 r_free = 0.4667 target = 0.177885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.150518 restraints weight = 18427.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.149943 restraints weight = 15231.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.150176 restraints weight = 13340.115| |-----------------------------------------------------------------------------| r_work (final): 0.4267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6290 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6495 Z= 0.183 Angle : 0.721 13.130 8750 Z= 0.358 Chirality : 0.045 0.235 999 Planarity : 0.004 0.068 1119 Dihedral : 5.873 22.273 838 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.50 % Allowed : 14.69 % Favored : 84.81 % Rotamer: Outliers : 3.14 % Allowed : 21.43 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -2.89 (0.28), residues: 803 helix: -0.74 (0.28), residues: 328 sheet: -1.95 (0.94), residues: 32 loop : -2.98 (0.27), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 805 HIS 0.002 0.001 HIS B 443 PHE 0.036 0.002 PHE B 111 TYR 0.010 0.001 TYR B 623 ARG 0.002 0.000 ARG B 400 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 49 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 280 ILE cc_start: 0.6928 (mt) cc_final: 0.6587 (mt) REVERT: B 414 THR cc_start: 0.6496 (OUTLIER) cc_final: 0.6152 (p) REVERT: B 483 ASP cc_start: 0.7322 (t0) cc_final: 0.6983 (t70) REVERT: B 633 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8216 (mmmm) REVERT: B 650 LEU cc_start: 0.7285 (OUTLIER) cc_final: 0.7045 (tp) REVERT: B 740 TYR cc_start: 0.7826 (OUTLIER) cc_final: 0.7232 (t80) outliers start: 22 outliers final: 16 residues processed: 68 average time/residue: 0.1511 time to fit residues: 15.0696 Evaluate side-chains 65 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 45 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 111 PHE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 216 HIS Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 465 MET Chi-restraints excluded: chain B residue 474 GLU Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 631 GLU Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 740 TYR Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 766 VAL Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 785 LYS Chi-restraints excluded: chain B residue 817 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 73 optimal weight: 0.4980 chunk 45 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 72 optimal weight: 0.0570 chunk 32 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 57 optimal weight: 0.5980 overall best weight: 0.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 402 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.176611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.148965 restraints weight = 18314.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.148712 restraints weight = 14777.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.148913 restraints weight = 12839.756| |-----------------------------------------------------------------------------| r_work (final): 0.4273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6333 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6495 Z= 0.219 Angle : 0.744 11.144 8750 Z= 0.372 Chirality : 0.045 0.205 999 Planarity : 0.005 0.068 1119 Dihedral : 5.976 22.075 838 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 17.94 Ramachandran Plot: Outliers : 0.50 % Allowed : 14.82 % Favored : 84.68 % Rotamer: Outliers : 2.86 % Allowed : 21.86 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -2.93 (0.28), residues: 803 helix: -0.77 (0.28), residues: 327 sheet: -1.98 (0.93), residues: 32 loop : -3.01 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 121 HIS 0.002 0.001 HIS B 216 PHE 0.036 0.002 PHE B 111 TYR 0.014 0.001 TYR B 206 ARG 0.002 0.000 ARG B 708 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 46 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 280 ILE cc_start: 0.6963 (mt) cc_final: 0.6614 (mt) REVERT: B 414 THR cc_start: 0.6480 (OUTLIER) cc_final: 0.6118 (p) REVERT: B 483 ASP cc_start: 0.7079 (t0) cc_final: 0.6822 (t0) REVERT: B 633 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.7897 (mmmt) REVERT: B 650 LEU cc_start: 0.7307 (OUTLIER) cc_final: 0.7001 (tp) REVERT: B 740 TYR cc_start: 0.7847 (OUTLIER) cc_final: 0.7160 (t80) outliers start: 20 outliers final: 16 residues processed: 63 average time/residue: 0.1481 time to fit residues: 13.7367 Evaluate side-chains 62 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 42 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 111 PHE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 216 HIS Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 465 MET Chi-restraints excluded: chain B residue 474 GLU Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 631 GLU Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 740 TYR Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 766 VAL Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 785 LYS Chi-restraints excluded: chain B residue 817 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 12 optimal weight: 0.4980 chunk 1 optimal weight: 10.0000 chunk 73 optimal weight: 0.4980 chunk 58 optimal weight: 0.4980 chunk 65 optimal weight: 0.9990 chunk 34 optimal weight: 7.9990 chunk 61 optimal weight: 0.7980 chunk 3 optimal weight: 0.0050 chunk 38 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 69 optimal weight: 0.7980 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4665 r_free = 0.4665 target = 0.177873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.151194 restraints weight = 18635.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.150231 restraints weight = 14592.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.150564 restraints weight = 13836.079| |-----------------------------------------------------------------------------| r_work (final): 0.4311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6272 moved from start: 0.4057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6495 Z= 0.184 Angle : 0.715 11.443 8750 Z= 0.357 Chirality : 0.045 0.230 999 Planarity : 0.004 0.069 1119 Dihedral : 5.815 21.429 838 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.50 % Allowed : 14.07 % Favored : 85.43 % Rotamer: Outliers : 3.00 % Allowed : 21.86 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -2.86 (0.28), residues: 803 helix: -0.70 (0.28), residues: 327 sheet: -1.91 (0.94), residues: 32 loop : -2.98 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 121 HIS 0.001 0.000 HIS B 216 PHE 0.036 0.002 PHE B 111 TYR 0.012 0.001 TYR B 206 ARG 0.002 0.000 ARG B 400 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2165.10 seconds wall clock time: 39 minutes 46.81 seconds (2386.81 seconds total)