Starting phenix.real_space_refine on Tue Mar 11 17:02:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a9b_15275/03_2025/8a9b_15275.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a9b_15275/03_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_15275/03_2025/8a9b_15275.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a9b_15275/03_2025/8a9b_15275.map" model { file = "/net/cci-nas-00/data/ceres_data/8a9b_15275/03_2025/8a9b_15275.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a9b_15275/03_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-5624/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: 4.28, per 1000 atoms: 0.67 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: 1.59 Conformation dependent library (CDL) restraints added in 941.0 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: 0.65 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: 1.86 Time building geometry restraints manager: 1.89 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: 0.700 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.030 Find NCS groups from input model: 0.060 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.220 ------------------------------------------------------------------------------- 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 : 0.809 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: 0.1958 time to fit residues: 19.6852 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 : 0.785 ------------------------------------------------------------------------------- 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 = 0.181868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.151982 restraints weight = 17365.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.152776 restraints weight = 13784.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.152902 restraints weight = 12908.822| |-----------------------------------------------------------------------------| r_work (final): 0.4296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6217 moved from start: 0.1368 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 : 6.165 35.651 838 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 17.09 Ramachandran Plot: Outliers : 0.87 % Allowed : 13.45 % Favored : 85.68 % 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 : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 183 GLN cc_start: 0.1417 (tm-30) cc_final: 0.1188 (tm-30) REVERT: B 294 MET cc_start: 0.6464 (mtt) cc_final: 0.5684 (mmp) REVERT: B 640 MET cc_start: 0.7797 (ptm) cc_final: 0.7317 (ptm) outliers start: 6 outliers final: 2 residues processed: 63 average time/residue: 0.1897 time to fit residues: 17.0095 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 : 0.767 ------------------------------------------------------------------------------- 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: 0.0170 chunk 46 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 62 optimal weight: 0.0970 overall best weight: 0.4818 ------------------------------------------------------------------------------- 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 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 849 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4713 r_free = 0.4713 target = 0.181977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.153456 restraints weight = 18110.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.153730 restraints weight = 15207.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.153761 restraints weight = 12477.799| |-----------------------------------------------------------------------------| r_work (final): 0.4311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6190 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6495 Z= 0.194 Angle : 0.746 9.897 8750 Z= 0.380 Chirality : 0.047 0.495 999 Planarity : 0.004 0.055 1119 Dihedral : 6.090 34.892 838 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.75 % Allowed : 12.58 % Favored : 86.67 % Rotamer: Outliers : 1.00 % Allowed : 13.43 % Favored : 85.57 % 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: -2.99 (0.28), residues: 803 helix: -0.87 (0.28), residues: 336 sheet: -2.57 (0.78), residues: 51 loop : -2.96 (0.28), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 805 HIS 0.001 0.001 HIS B 216 PHE 0.026 0.002 PHE B 854 TYR 0.015 0.001 TYR B 187 ARG 0.002 0.000 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 58 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 185 PHE cc_start: 0.6419 (t80) cc_final: 0.6136 (t80) REVERT: B 294 MET cc_start: 0.6354 (mtt) cc_final: 0.5657 (mmp) REVERT: B 640 MET cc_start: 0.7979 (ptm) cc_final: 0.7459 (ptm) outliers start: 7 outliers final: 5 residues processed: 56 average time/residue: 0.1614 time to fit residues: 13.6857 Evaluate side-chains 47 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 436 VAL 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: 1.9990 chunk 62 optimal weight: 0.0060 chunk 72 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 61 optimal weight: 0.0370 chunk 1 optimal weight: 10.0000 chunk 51 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 2 optimal weight: 0.0970 chunk 31 optimal weight: 1.9990 overall best weight: 0.4072 ------------------------------------------------------------------------------- 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 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 = 0.4718 r_free = 0.4718 target = 0.182411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.154304 restraints weight = 18353.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.155030 restraints weight = 14763.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.154866 restraints weight = 11763.234| |-----------------------------------------------------------------------------| r_work (final): 0.4332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6135 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6495 Z= 0.177 Angle : 0.724 12.528 8750 Z= 0.364 Chirality : 0.045 0.247 999 Planarity : 0.004 0.058 1119 Dihedral : 5.756 25.082 838 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.62 % Allowed : 13.20 % Favored : 86.18 % Rotamer: Outliers : 1.71 % Allowed : 15.57 % Favored : 82.71 % 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: -2.87 (0.28), residues: 803 helix: -0.75 (0.28), residues: 332 sheet: -2.60 (0.77), residues: 51 loop : -2.88 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 805 HIS 0.001 0.001 HIS B 216 PHE 0.036 0.002 PHE B 111 TYR 0.012 0.001 TYR B 187 ARG 0.004 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 62 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 50 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 375 PRO cc_start: 0.4420 (Cg_endo) cc_final: 0.3624 (Cg_exo) REVERT: B 447 LEU cc_start: 0.7967 (mm) cc_final: 0.7436 (tp) REVERT: B 465 MET cc_start: 0.4738 (OUTLIER) cc_final: 0.4045 (mtm) REVERT: B 640 MET cc_start: 0.7930 (ptm) cc_final: 0.7379 (ptm) outliers start: 12 outliers final: 7 residues processed: 60 average time/residue: 0.1660 time to fit residues: 14.4574 Evaluate side-chains 51 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.755 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 21 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 71 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 0.4980 chunk 6 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- 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 863 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4634 r_free = 0.4634 target = 0.175096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.146693 restraints weight = 17987.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.146850 restraints weight = 15908.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.146727 restraints weight = 12973.382| |-----------------------------------------------------------------------------| r_work (final): 0.4251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6363 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 6495 Z= 0.345 Angle : 0.839 10.562 8750 Z= 0.429 Chirality : 0.048 0.242 999 Planarity : 0.005 0.063 1119 Dihedral : 6.392 26.949 838 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 22.00 Ramachandran Plot: Outliers : 0.62 % Allowed : 14.82 % Favored : 84.56 % Rotamer: Outliers : 2.57 % Allowed : 18.43 % Favored : 79.00 % 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: -3.24 (0.27), residues: 803 helix: -0.98 (0.27), residues: 332 sheet: -2.70 (0.85), residues: 33 loop : -3.20 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 121 HIS 0.004 0.002 HIS B 216 PHE 0.035 0.003 PHE B 111 TYR 0.017 0.002 TYR B 751 ARG 0.005 0.001 ARG B 331 *********************** 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 68 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 50 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 LYS cc_start: 0.7130 (OUTLIER) cc_final: 0.6424 (tptp) REVERT: B 483 ASP cc_start: 0.6416 (t0) cc_final: 0.6064 (t0) REVERT: B 579 LYS cc_start: 0.7158 (ptmt) cc_final: 0.6956 (pttp) REVERT: B 669 ASP cc_start: 0.7660 (m-30) cc_final: 0.6913 (p0) outliers start: 18 outliers final: 12 residues processed: 63 average time/residue: 0.1464 time to fit residues: 13.6017 Evaluate side-chains 58 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 LYS 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 4 optimal weight: 1.9990 chunk 52 optimal weight: 0.0980 chunk 29 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 19 optimal weight: 0.2980 chunk 72 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 53 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- 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 = 0.4669 r_free = 0.4669 target = 0.177945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.150949 restraints weight = 18077.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.150664 restraints weight = 15988.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.150711 restraints weight = 12830.862| |-----------------------------------------------------------------------------| r_work (final): 0.4309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6242 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6495 Z= 0.215 Angle : 0.739 9.413 8750 Z= 0.372 Chirality : 0.045 0.226 999 Planarity : 0.005 0.066 1119 Dihedral : 6.111 26.092 838 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 17.16 Ramachandran Plot: Outliers : 0.62 % Allowed : 13.70 % Favored : 85.68 % Rotamer: Outliers : 2.86 % Allowed : 19.14 % Favored : 78.00 % 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: -3.09 (0.27), residues: 803 helix: -0.84 (0.28), residues: 327 sheet: -2.78 (0.92), residues: 25 loop : -3.10 (0.26), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 805 HIS 0.001 0.001 HIS B 580 PHE 0.031 0.002 PHE B 111 TYR 0.012 0.001 TYR B 623 ARG 0.002 0.000 ARG B 708 *********************** 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 74 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 54 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 183 GLN cc_start: 0.1646 (tm-30) cc_final: 0.1184 (tm-30) REVERT: B 280 ILE cc_start: 0.7088 (mt) cc_final: 0.6820 (mt) REVERT: B 357 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8491 (tp) REVERT: B 414 THR cc_start: 0.6415 (OUTLIER) cc_final: 0.6067 (p) REVERT: B 483 ASP cc_start: 0.6217 (t0) cc_final: 0.5737 (t70) REVERT: B 579 LYS cc_start: 0.7107 (ptmt) cc_final: 0.6865 (pttp) outliers start: 20 outliers final: 13 residues processed: 69 average time/residue: 0.1613 time to fit residues: 16.3880 Evaluate side-chains 62 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 47 time to evaluate : 0.790 ------------------------------------------------------------------------------- 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 357 LEU 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 701 ILE 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 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: 8.9990 chunk 65 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 42 optimal weight: 0.3980 chunk 31 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 48 optimal weight: 0.8980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.4647 r_free = 0.4647 target = 0.176094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.147610 restraints weight = 18038.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.147831 restraints weight = 17283.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.147920 restraints weight = 14255.636| |-----------------------------------------------------------------------------| r_work (final): 0.4236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6336 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6495 Z= 0.240 Angle : 0.768 11.288 8750 Z= 0.388 Chirality : 0.046 0.228 999 Planarity : 0.005 0.067 1119 Dihedral : 6.147 24.804 838 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 18.18 Ramachandran Plot: Outliers : 0.50 % Allowed : 15.44 % Favored : 84.06 % Rotamer: Outliers : 3.00 % Allowed : 20.86 % Favored : 76.14 % 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: -3.13 (0.27), residues: 803 helix: -0.93 (0.28), residues: 326 sheet: -2.46 (0.89), residues: 32 loop : -3.08 (0.27), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 121 HIS 0.001 0.000 HIS B 266 PHE 0.034 0.002 PHE B 111 TYR 0.012 0.001 TYR B 187 ARG 0.003 0.001 ARG B 140 *********************** 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 72 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 51 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 280 ILE cc_start: 0.6968 (mt) cc_final: 0.6609 (mt) REVERT: B 357 LEU cc_start: 0.8660 (tt) cc_final: 0.8412 (tp) REVERT: B 414 THR cc_start: 0.6485 (OUTLIER) cc_final: 0.6143 (p) REVERT: B 483 ASP cc_start: 0.6399 (t0) cc_final: 0.5890 (t70) REVERT: B 669 ASP cc_start: 0.7200 (m-30) cc_final: 0.6430 (p0) REVERT: B 740 TYR cc_start: 0.8057 (OUTLIER) cc_final: 0.7494 (t80) outliers start: 21 outliers final: 16 residues processed: 69 average time/residue: 0.1520 time to fit residues: 15.6879 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 : 0.713 ------------------------------------------------------------------------------- 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 414 THR 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 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 Chi-restraints excluded: chain B residue 851 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 21 optimal weight: 0.7980 chunk 10 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 54 optimal weight: 0.0980 chunk 79 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4656 r_free = 0.4656 target = 0.176833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.149494 restraints weight = 17871.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.149101 restraints weight = 15525.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.148920 restraints weight = 13142.345| |-----------------------------------------------------------------------------| r_work (final): 0.4252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6310 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6495 Z= 0.217 Angle : 0.762 12.635 8750 Z= 0.379 Chirality : 0.046 0.216 999 Planarity : 0.005 0.067 1119 Dihedral : 6.038 24.285 838 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 18.26 Ramachandran Plot: Outliers : 0.50 % Allowed : 14.07 % Favored : 85.43 % Rotamer: Outliers : 2.43 % Allowed : 22.29 % 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: -3.04 (0.28), residues: 803 helix: -0.86 (0.28), residues: 327 sheet: -2.37 (0.88), residues: 32 loop : -3.04 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 121 HIS 0.001 0.000 HIS B 266 PHE 0.034 0.002 PHE B 111 TYR 0.011 0.001 TYR B 187 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 63 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 46 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 280 ILE cc_start: 0.7036 (mt) cc_final: 0.6691 (mt) REVERT: B 357 LEU cc_start: 0.8667 (tt) cc_final: 0.8417 (tp) REVERT: B 414 THR cc_start: 0.6474 (OUTLIER) cc_final: 0.6131 (p) REVERT: B 483 ASP cc_start: 0.6528 (t0) cc_final: 0.6016 (t70) REVERT: B 640 MET cc_start: 0.8109 (ptm) cc_final: 0.7592 (ptm) REVERT: B 669 ASP cc_start: 0.7234 (m-30) cc_final: 0.6422 (p0) REVERT: B 740 TYR cc_start: 0.8084 (OUTLIER) cc_final: 0.7503 (t80) outliers start: 17 outliers final: 14 residues processed: 59 average time/residue: 0.1415 time to fit residues: 12.6944 Evaluate side-chains 61 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 45 time to evaluate : 0.753 ------------------------------------------------------------------------------- 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 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 701 ILE 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: 0.7980 chunk 10 optimal weight: 9.9990 chunk 57 optimal weight: 0.1980 chunk 56 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 9 optimal weight: 0.2980 chunk 67 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 2 optimal weight: 0.4980 chunk 45 optimal weight: 3.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.4657 r_free = 0.4657 target = 0.176942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.148877 restraints weight = 18225.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.149248 restraints weight = 14978.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.149343 restraints weight = 12641.714| |-----------------------------------------------------------------------------| r_work (final): 0.4283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6271 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6495 Z= 0.195 Angle : 0.739 13.574 8750 Z= 0.366 Chirality : 0.045 0.239 999 Planarity : 0.005 0.069 1119 Dihedral : 5.910 22.962 838 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.50 % Allowed : 14.20 % Favored : 85.31 % Rotamer: Outliers : 3.00 % Allowed : 22.00 % Favored : 75.00 % 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: -0.84 (0.28), residues: 328 sheet: -2.25 (0.90), residues: 32 loop : -3.00 (0.27), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 121 HIS 0.003 0.001 HIS B 443 PHE 0.035 0.002 PHE B 111 TYR 0.010 0.001 TYR B 187 ARG 0.002 0.000 ARG B 708 *********************** 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 69 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 48 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 280 ILE cc_start: 0.6863 (mt) cc_final: 0.6503 (mt) REVERT: B 357 LEU cc_start: 0.8594 (tt) cc_final: 0.8261 (tp) REVERT: B 414 THR cc_start: 0.6412 (OUTLIER) cc_final: 0.6089 (p) REVERT: B 483 ASP cc_start: 0.7219 (t0) cc_final: 0.6897 (t70) REVERT: B 640 MET cc_start: 0.8144 (ptm) cc_final: 0.7637 (ptm) REVERT: B 642 GLU cc_start: 0.7646 (mt-10) cc_final: 0.6936 (mt-10) REVERT: B 669 ASP cc_start: 0.6801 (m-30) cc_final: 0.6146 (p0) REVERT: B 740 TYR cc_start: 0.7981 (OUTLIER) cc_final: 0.7444 (t80) outliers start: 21 outliers final: 14 residues processed: 66 average time/residue: 0.1382 time to fit residues: 13.7308 Evaluate side-chains 61 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 45 time to evaluate : 0.688 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 72 optimal weight: 0.5980 chunk 32 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 33 optimal weight: 9.9990 chunk 57 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4628 r_free = 0.4628 target = 0.174463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.143816 restraints weight = 18297.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.145415 restraints weight = 13933.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.146268 restraints weight = 11524.884| |-----------------------------------------------------------------------------| r_work (final): 0.4239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6401 moved from start: 0.3865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6495 Z= 0.260 Angle : 0.780 13.501 8750 Z= 0.393 Chirality : 0.047 0.216 999 Planarity : 0.005 0.066 1119 Dihedral : 6.169 23.004 838 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 18.88 Ramachandran Plot: Outliers : 0.50 % Allowed : 15.07 % Favored : 84.43 % Rotamer: Outliers : 2.43 % Allowed : 22.71 % Favored : 74.86 % 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: -3.15 (0.27), residues: 803 helix: -0.94 (0.27), residues: 327 sheet: -2.45 (0.87), residues: 32 loop : -3.11 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 121 HIS 0.002 0.001 HIS B 443 PHE 0.035 0.002 PHE B 111 TYR 0.014 0.002 TYR B 206 ARG 0.003 0.001 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: 17 poor density : 49 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 280 ILE cc_start: 0.7162 (mt) cc_final: 0.6814 (mt) REVERT: B 357 LEU cc_start: 0.8644 (tt) cc_final: 0.8387 (tp) REVERT: B 414 THR cc_start: 0.6502 (OUTLIER) cc_final: 0.6138 (p) REVERT: B 483 ASP cc_start: 0.6625 (t0) cc_final: 0.6286 (t0) REVERT: B 642 GLU cc_start: 0.7488 (mt-10) cc_final: 0.6985 (mt-10) REVERT: B 669 ASP cc_start: 0.6745 (m-30) cc_final: 0.6094 (p0) REVERT: B 740 TYR cc_start: 0.8156 (OUTLIER) cc_final: 0.7535 (t80) outliers start: 17 outliers final: 14 residues processed: 63 average time/residue: 0.1473 time to fit residues: 13.9719 Evaluate side-chains 63 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 47 time to evaluate : 0.795 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 12 optimal weight: 0.7980 chunk 1 optimal weight: 9.9990 chunk 73 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 65 optimal weight: 0.3980 chunk 34 optimal weight: 7.9990 chunk 61 optimal weight: 0.4980 chunk 3 optimal weight: 0.0980 chunk 38 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 367 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 = 0.4651 r_free = 0.4651 target = 0.176473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.146914 restraints weight = 18575.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.148560 restraints weight = 14710.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.148623 restraints weight = 11276.650| |-----------------------------------------------------------------------------| r_work (final): 0.4243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6362 moved from start: 0.4003 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= 0.193 Angle : 0.728 10.995 8750 Z= 0.363 Chirality : 0.045 0.229 999 Planarity : 0.005 0.069 1119 Dihedral : 5.977 22.195 838 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 17.09 Ramachandran Plot: Outliers : 0.50 % Allowed : 14.32 % Favored : 85.18 % Rotamer: Outliers : 2.57 % Allowed : 22.43 % Favored : 75.00 % 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: -3.02 (0.28), residues: 803 helix: -0.87 (0.28), residues: 327 sheet: -2.29 (0.89), residues: 32 loop : -3.01 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 805 HIS 0.001 0.000 HIS B 580 PHE 0.035 0.002 PHE B 111 TYR 0.012 0.001 TYR B 751 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: 2252.43 seconds wall clock time: 39 minutes 59.26 seconds (2399.26 seconds total)