Starting phenix.real_space_refine on Fri Dec 8 00:50:19 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rav_24387/12_2023/7rav_24387_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rav_24387/12_2023/7rav_24387.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rav_24387/12_2023/7rav_24387.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rav_24387/12_2023/7rav_24387.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rav_24387/12_2023/7rav_24387_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rav_24387/12_2023/7rav_24387_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 40 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 39 5.16 5 C 3976 2.51 5 N 1046 2.21 5 O 1151 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 60": "OE1" <-> "OE2" Residue "A PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 123": "OE1" <-> "OE2" Residue "A GLU 158": "OE1" <-> "OE2" Residue "A GLU 159": "OE1" <-> "OE2" Residue "A PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 168": "OD1" <-> "OD2" Residue "A GLU 208": "OE1" <-> "OE2" Residue "A GLU 216": "OE1" <-> "OE2" Residue "A ASP 272": "OD1" <-> "OD2" Residue "A GLU 279": "OE1" <-> "OE2" Residue "A GLU 471": "OE1" <-> "OE2" Residue "A ASP 551": "OD1" <-> "OD2" Residue "A ASP 588": "OD1" <-> "OD2" Residue "A TYR 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 628": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 631": "OD1" <-> "OD2" Residue "A ASP 634": "OD1" <-> "OD2" Residue "A PHE 644": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 706": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 748": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 751": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 764": "OD1" <-> "OD2" Residue "A TYR 795": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 6215 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 6215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 774, 6215 Unusual residues: {'ATP': 1} Classifications: {'peptide': 773, 'undetermined': 1} Link IDs: {'PTRANS': 26, 'TRANS': 746, None: 1} Not linked: pdbres="ARG A 915 " pdbres="ATP A1501 " Chain breaks: 3 Time building chain proxies: 3.99, per 1000 atoms: 0.64 Number of scatterers: 6215 At special positions: 0 Unit cell: (74.858, 78.0662, 133.675, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 39 16.00 P 3 15.00 O 1151 8.00 N 1046 7.00 C 3976 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 124 " distance=2.03 Simple disulfide: pdb=" SG CYS A 200 " - pdb=" SG CYS A 224 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 2.43 Conformation dependent library (CDL) restraints added in 1.2 seconds 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1460 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 34 helices and 3 sheets defined 40.1% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.43 Creating SS restraints... Processing helix chain 'A' and resid 65 through 69 removed outlier: 4.092A pdb=" N THR A 69 " --> pdb=" O THR A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 84 Processing helix chain 'A' and resid 113 through 120 Processing helix chain 'A' and resid 160 through 164 Processing helix chain 'A' and resid 178 through 184 removed outlier: 3.826A pdb=" N ALA A 184 " --> pdb=" O VAL A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 220 Processing helix chain 'A' and resid 225 through 230 Processing helix chain 'A' and resid 235 through 239 Processing helix chain 'A' and resid 275 through 281 removed outlier: 4.022A pdb=" N LEU A 280 " --> pdb=" O ALA A 276 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ARG A 281 " --> pdb=" O ASN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 300 Processing helix chain 'A' and resid 333 through 339 Processing helix chain 'A' and resid 343 through 349 Processing helix chain 'A' and resid 402 through 417 Processing helix chain 'A' and resid 455 through 461 removed outlier: 3.711A pdb=" N PHE A 459 " --> pdb=" O ILE A 455 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N SER A 460 " --> pdb=" O PRO A 456 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASN A 461 " --> pdb=" O GLU A 457 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 455 through 461' Processing helix chain 'A' and resid 476 through 488 Processing helix chain 'A' and resid 493 through 497 removed outlier: 3.803A pdb=" N ARG A 497 " --> pdb=" O LEU A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 520 Processing helix chain 'A' and resid 532 through 541 Processing helix chain 'A' and resid 556 through 558 No H-bonds generated for 'chain 'A' and resid 556 through 558' Processing helix chain 'A' and resid 561 through 568 Processing helix chain 'A' and resid 604 through 614 Processing helix chain 'A' and resid 620 through 629 Processing helix chain 'A' and resid 642 through 653 Processing helix chain 'A' and resid 663 through 703 removed outlier: 3.880A pdb=" N LYS A 680 " --> pdb=" O SER A 676 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N ALA A 681 " --> pdb=" O LEU A 677 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N THR A 682 " --> pdb=" O LYS A 678 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N GLU A 684 " --> pdb=" O LYS A 680 " (cutoff:3.500A) Proline residue: A 685 - end of helix removed outlier: 3.916A pdb=" N LEU A 696 " --> pdb=" O SER A 692 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA A 697 " --> pdb=" O CYS A 693 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N PHE A 702 " --> pdb=" O LEU A 698 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER A 703 " --> pdb=" O THR A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 716 removed outlier: 3.749A pdb=" N ALA A 714 " --> pdb=" O SER A 710 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU A 715 " --> pdb=" O ASP A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 727 Processing helix chain 'A' and resid 746 through 762 Processing helix chain 'A' and resid 766 through 777 removed outlier: 4.432A pdb=" N LEU A 771 " --> pdb=" O GLU A 767 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLY A 772 " --> pdb=" O ASP A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 787 Processing helix chain 'A' and resid 793 through 796 No H-bonds generated for 'chain 'A' and resid 793 through 796' Processing helix chain 'A' and resid 802 through 815 Proline residue: A 806 - end of helix removed outlier: 3.835A pdb=" N LEU A 815 " --> pdb=" O HIS A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 877 removed outlier: 3.993A pdb=" N THR A 877 " --> pdb=" O TYR A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 881 through 886 removed outlier: 4.224A pdb=" N ILE A 885 " --> pdb=" O CYS A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 913 No H-bonds generated for 'chain 'A' and resid 911 through 913' Processing sheet with id= A, first strand: chain 'A' and resid 86 through 88 Processing sheet with id= B, first strand: chain 'A' and resid 186 through 188 Processing sheet with id= C, first strand: chain 'A' and resid 466 through 468 removed outlier: 6.813A pdb=" N LEU A 500 " --> pdb=" O LEU A 547 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N LEU A 549 " --> pdb=" O LEU A 500 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N PHE A 502 " --> pdb=" O LEU A 549 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N ASP A 551 " --> pdb=" O PHE A 502 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LEU A 504 " --> pdb=" O ASP A 551 " (cutoff:3.500A) 168 hydrogen bonds defined for protein. 444 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: 1.70 Time building geometry restraints manager: 2.64 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: 1961 1.34 - 1.46: 1377 1.46 - 1.58: 2962 1.58 - 1.70: 5 1.70 - 1.83: 52 Bond restraints: 6357 Sorted by residual: bond pdb=" C4 ATP A1501 " pdb=" C5 ATP A1501 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.24e+01 bond pdb=" C5 ATP A1501 " pdb=" C6 ATP A1501 " ideal model delta sigma weight residual 1.409 1.478 -0.069 1.00e-02 1.00e+04 4.79e+01 bond pdb=" C8 ATP A1501 " pdb=" N7 ATP A1501 " ideal model delta sigma weight residual 1.310 1.356 -0.046 1.00e-02 1.00e+04 2.11e+01 bond pdb=" C5 ATP A1501 " pdb=" N7 ATP A1501 " ideal model delta sigma weight residual 1.387 1.342 0.045 1.00e-02 1.00e+04 2.01e+01 bond pdb=" C4 ATP A1501 " pdb=" N9 ATP A1501 " ideal model delta sigma weight residual 1.374 1.331 0.043 1.00e-02 1.00e+04 1.89e+01 ... (remaining 6352 not shown) Histogram of bond angle deviations from ideal: 99.15 - 106.53: 158 106.53 - 113.91: 3493 113.91 - 121.28: 3388 121.28 - 128.66: 1506 128.66 - 136.04: 48 Bond angle restraints: 8593 Sorted by residual: angle pdb=" PB ATP A1501 " pdb=" O3B ATP A1501 " pdb=" PG ATP A1501 " ideal model delta sigma weight residual 139.87 119.24 20.63 1.00e+00 1.00e+00 4.26e+02 angle pdb=" PA ATP A1501 " pdb=" O3A ATP A1501 " pdb=" PB ATP A1501 " ideal model delta sigma weight residual 136.83 118.98 17.85 1.00e+00 1.00e+00 3.19e+02 angle pdb=" N GLY A 175 " pdb=" CA GLY A 175 " pdb=" C GLY A 175 " ideal model delta sigma weight residual 112.73 100.90 11.83 1.20e+00 6.94e-01 9.72e+01 angle pdb=" C5 ATP A1501 " pdb=" C4 ATP A1501 " pdb=" N3 ATP A1501 " ideal model delta sigma weight residual 126.80 118.66 8.14 1.00e+00 1.00e+00 6.62e+01 angle pdb=" N3 ATP A1501 " pdb=" C4 ATP A1501 " pdb=" N9 ATP A1501 " ideal model delta sigma weight residual 127.04 134.79 -7.75 1.15e+00 7.59e-01 4.56e+01 ... (remaining 8588 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 3348 17.97 - 35.93: 371 35.93 - 53.90: 71 53.90 - 71.86: 15 71.86 - 89.83: 11 Dihedral angle restraints: 3816 sinusoidal: 1559 harmonic: 2257 Sorted by residual: dihedral pdb=" CB CYS A 100 " pdb=" SG CYS A 100 " pdb=" SG CYS A 124 " pdb=" CB CYS A 124 " ideal model delta sinusoidal sigma weight residual 93.00 48.56 44.44 1 1.00e+01 1.00e-02 2.75e+01 dihedral pdb=" CA HIS A 157 " pdb=" C HIS A 157 " pdb=" N GLU A 158 " pdb=" CA GLU A 158 " ideal model delta harmonic sigma weight residual -180.00 -154.55 -25.45 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA ILE A 135 " pdb=" C ILE A 135 " pdb=" N GLY A 136 " pdb=" CA GLY A 136 " ideal model delta harmonic sigma weight residual 180.00 156.40 23.60 0 5.00e+00 4.00e-02 2.23e+01 ... (remaining 3813 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 756 0.058 - 0.117: 170 0.117 - 0.175: 18 0.175 - 0.233: 2 0.233 - 0.292: 1 Chirality restraints: 947 Sorted by residual: chirality pdb=" CA PRO A 340 " pdb=" N PRO A 340 " pdb=" C PRO A 340 " pdb=" CB PRO A 340 " both_signs ideal model delta sigma weight residual False 2.72 2.43 0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CA HIS A 174 " pdb=" N HIS A 174 " pdb=" C HIS A 174 " pdb=" CB HIS A 174 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.05e-01 chirality pdb=" CA GLN A 766 " pdb=" N GLN A 766 " pdb=" C GLN A 766 " pdb=" CB GLN A 766 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.68e-01 ... (remaining 944 not shown) Planarity restraints: 1089 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 339 " 0.061 5.00e-02 4.00e+02 9.20e-02 1.36e+01 pdb=" N PRO A 340 " -0.159 5.00e-02 4.00e+02 pdb=" CA PRO A 340 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 340 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 492 " -0.038 5.00e-02 4.00e+02 5.85e-02 5.48e+00 pdb=" N PRO A 493 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 493 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 493 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 330 " 0.037 5.00e-02 4.00e+02 5.58e-02 4.97e+00 pdb=" N PRO A 331 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 331 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 331 " 0.032 5.00e-02 4.00e+02 ... (remaining 1086 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1072 2.76 - 3.29: 6549 3.29 - 3.83: 9935 3.83 - 4.36: 11671 4.36 - 4.90: 18886 Nonbonded interactions: 48113 Sorted by model distance: nonbonded pdb=" OH TYR A 172 " pdb=" NH2 ARG A 261 " model vdw 2.224 2.520 nonbonded pdb=" NZ LYS A 723 " pdb=" OG1 THR A 725 " model vdw 2.224 2.520 nonbonded pdb=" NH1 ARG A 314 " pdb=" O THR A 430 " model vdw 2.242 2.520 nonbonded pdb=" OG SER A 554 " pdb=" OG SER A 558 " model vdw 2.247 2.440 nonbonded pdb=" O ASN A 900 " pdb=" ND2 ASN A 900 " model vdw 2.248 2.520 ... (remaining 48108 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 3.670 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 21.480 Find NCS groups from input model: 0.170 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:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 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 0.079 6357 Z= 0.275 Angle : 0.930 20.628 8593 Z= 0.590 Chirality : 0.049 0.292 947 Planarity : 0.005 0.092 1089 Dihedral : 15.924 89.826 2350 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.39 % Allowed : 16.73 % Favored : 82.88 % Rotamer: Outliers : 1.17 % Allowed : 0.44 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.36 (0.29), residues: 765 helix: -0.98 (0.29), residues: 313 sheet: -1.74 (0.75), residues: 37 loop : -3.46 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 220 HIS 0.006 0.001 HIS A 582 PHE 0.027 0.002 PHE A 859 TYR 0.037 0.002 TYR A 496 ARG 0.008 0.001 ARG A 74 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 225 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 0 residues processed: 228 average time/residue: 0.2120 time to fit residues: 60.8742 Evaluate side-chains 196 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 196 time to evaluate : 0.658 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 65 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 39 optimal weight: 0.4980 chunk 31 optimal weight: 0.0020 chunk 60 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 overall best weight: 0.8994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 ASN A 570 ASN A 900 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 6357 Z= 0.295 Angle : 0.795 10.742 8593 Z= 0.411 Chirality : 0.049 0.247 947 Planarity : 0.005 0.049 1089 Dihedral : 7.940 85.153 871 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 17.25 Ramachandran Plot: Outliers : 0.39 % Allowed : 17.25 % Favored : 82.35 % Rotamer: Outliers : 1.90 % Allowed : 15.96 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % 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: -3.16 (0.30), residues: 765 helix: -0.71 (0.30), residues: 329 sheet: -1.78 (0.69), residues: 42 loop : -3.52 (0.29), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 220 HIS 0.005 0.001 HIS A 253 PHE 0.052 0.002 PHE A 792 TYR 0.043 0.003 TYR A 496 ARG 0.008 0.001 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 214 time to evaluate : 0.701 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 9 residues processed: 220 average time/residue: 0.2181 time to fit residues: 60.2724 Evaluate side-chains 212 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 203 time to evaluate : 0.704 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0987 time to fit residues: 2.3070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 38 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 19 optimal weight: 0.0070 chunk 70 optimal weight: 0.4980 chunk 75 optimal weight: 0.9990 chunk 62 optimal weight: 0.0270 chunk 69 optimal weight: 0.3980 chunk 23 optimal weight: 0.7980 chunk 56 optimal weight: 0.5980 overall best weight: 0.3056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 ASN A 900 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6357 Z= 0.183 Angle : 0.724 9.122 8593 Z= 0.367 Chirality : 0.044 0.167 947 Planarity : 0.004 0.044 1089 Dihedral : 7.549 87.034 871 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.26 % Allowed : 15.69 % Favored : 84.05 % Rotamer: Outliers : 1.02 % Allowed : 22.11 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.30), residues: 765 helix: -0.43 (0.31), residues: 315 sheet: -1.74 (0.72), residues: 37 loop : -3.43 (0.28), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 220 HIS 0.004 0.001 HIS A 582 PHE 0.036 0.002 PHE A 792 TYR 0.023 0.002 TYR A 496 ARG 0.005 0.001 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 210 time to evaluate : 0.710 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 212 average time/residue: 0.2282 time to fit residues: 60.8582 Evaluate side-chains 201 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 200 time to evaluate : 0.703 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0592 time to fit residues: 1.1025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 69 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 ASN ** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 ASN A 606 ASN A 900 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6357 Z= 0.275 Angle : 0.769 11.006 8593 Z= 0.392 Chirality : 0.047 0.246 947 Planarity : 0.005 0.073 1089 Dihedral : 7.599 76.802 871 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 17.00 Ramachandran Plot: Outliers : 0.13 % Allowed : 17.25 % Favored : 82.61 % Rotamer: Outliers : 3.07 % Allowed : 23.13 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % 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: -3.00 (0.30), residues: 765 helix: -0.45 (0.30), residues: 321 sheet: -1.81 (0.67), residues: 42 loop : -3.51 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 220 HIS 0.004 0.001 HIS A 444 PHE 0.031 0.002 PHE A 226 TYR 0.021 0.002 TYR A 605 ARG 0.010 0.001 ARG A 92 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 206 time to evaluate : 0.739 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 8 residues processed: 214 average time/residue: 0.2262 time to fit residues: 61.0547 Evaluate side-chains 206 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 198 time to evaluate : 0.744 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1021 time to fit residues: 2.2338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 42 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 63 optimal weight: 0.4980 chunk 51 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 18 optimal weight: 0.3980 chunk 25 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 461 ASN A 570 ASN A 606 ASN A 695 GLN A 900 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6357 Z= 0.260 Angle : 0.767 10.668 8593 Z= 0.387 Chirality : 0.048 0.290 947 Planarity : 0.005 0.060 1089 Dihedral : 7.549 73.617 871 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.13 % Allowed : 17.39 % Favored : 82.48 % Rotamer: Outliers : 1.76 % Allowed : 25.18 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % 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 (0.30), residues: 765 helix: -0.35 (0.31), residues: 315 sheet: -1.85 (0.65), residues: 42 loop : -3.51 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 220 HIS 0.004 0.001 HIS A 174 PHE 0.023 0.002 PHE A 792 TYR 0.023 0.002 TYR A 639 ARG 0.007 0.001 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 200 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 205 average time/residue: 0.2225 time to fit residues: 57.3527 Evaluate side-chains 199 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 194 time to evaluate : 0.772 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1730 time to fit residues: 2.1470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 67 optimal weight: 0.6980 chunk 14 optimal weight: 0.0870 chunk 43 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 61 optimal weight: 0.0060 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 39 optimal weight: 0.1980 chunk 71 optimal weight: 0.2980 overall best weight: 0.2574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 ASN ** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 ASN A 695 GLN A 900 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6357 Z= 0.178 Angle : 0.742 13.019 8593 Z= 0.371 Chirality : 0.046 0.344 947 Planarity : 0.004 0.049 1089 Dihedral : 7.216 77.036 871 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.13 % Allowed : 15.42 % Favored : 84.44 % Rotamer: Outliers : 2.05 % Allowed : 25.62 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.92 (0.30), residues: 765 helix: -0.40 (0.30), residues: 315 sheet: -1.62 (0.70), residues: 37 loop : -3.41 (0.28), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 220 HIS 0.004 0.001 HIS A 582 PHE 0.020 0.001 PHE A 792 TYR 0.021 0.002 TYR A 903 ARG 0.004 0.001 ARG A 179 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 206 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 9 residues processed: 213 average time/residue: 0.2206 time to fit residues: 59.4387 Evaluate side-chains 208 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 199 time to evaluate : 0.738 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0674 time to fit residues: 2.1308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 8 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 54 optimal weight: 0.5980 chunk 62 optimal weight: 0.5980 chunk 41 optimal weight: 0.5980 chunk 74 optimal weight: 0.0000 chunk 46 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 34 optimal weight: 0.0010 chunk 29 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6357 Z= 0.197 Angle : 0.753 12.746 8593 Z= 0.376 Chirality : 0.048 0.377 947 Planarity : 0.004 0.047 1089 Dihedral : 7.024 74.088 871 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.13 % Allowed : 15.82 % Favored : 84.05 % Rotamer: Outliers : 0.88 % Allowed : 27.96 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.88 (0.30), residues: 765 helix: -0.33 (0.30), residues: 314 sheet: -1.66 (0.72), residues: 37 loop : -3.40 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 220 HIS 0.004 0.001 HIS A 582 PHE 0.019 0.001 PHE A 792 TYR 0.019 0.002 TYR A 903 ARG 0.006 0.001 ARG A 92 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 197 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 199 average time/residue: 0.2287 time to fit residues: 56.9079 Evaluate side-chains 197 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 195 time to evaluate : 0.789 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0727 time to fit residues: 1.2917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 22 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 6 optimal weight: 0.3980 chunk 58 optimal weight: 0.4980 chunk 67 optimal weight: 0.0470 chunk 71 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6357 Z= 0.220 Angle : 0.784 12.930 8593 Z= 0.392 Chirality : 0.049 0.366 947 Planarity : 0.004 0.044 1089 Dihedral : 7.066 71.451 871 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.13 % Allowed : 15.56 % Favored : 84.31 % Rotamer: Outliers : 0.88 % Allowed : 28.99 % Favored : 70.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.88 (0.30), residues: 765 helix: -0.27 (0.30), residues: 315 sheet: -1.72 (0.72), residues: 37 loop : -3.45 (0.28), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 220 HIS 0.004 0.001 HIS A 582 PHE 0.019 0.001 PHE A 792 TYR 0.019 0.002 TYR A 605 ARG 0.007 0.001 ARG A 92 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 194 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 198 average time/residue: 0.2204 time to fit residues: 54.7955 Evaluate side-chains 190 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 187 time to evaluate : 0.718 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0738 time to fit residues: 1.3890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 71 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 chunk 65 optimal weight: 0.5980 chunk 68 optimal weight: 0.0050 chunk 45 optimal weight: 0.9990 chunk 73 optimal weight: 0.0050 chunk 44 optimal weight: 1.9990 overall best weight: 0.4008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6357 Z= 0.209 Angle : 0.799 13.173 8593 Z= 0.399 Chirality : 0.049 0.377 947 Planarity : 0.004 0.044 1089 Dihedral : 7.003 72.249 871 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.13 % Allowed : 15.82 % Favored : 84.05 % Rotamer: Outliers : 1.46 % Allowed : 28.55 % Favored : 69.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.29), residues: 765 helix: -0.31 (0.30), residues: 315 sheet: -1.71 (0.71), residues: 37 loop : -3.40 (0.28), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 220 HIS 0.005 0.001 HIS A 811 PHE 0.029 0.001 PHE A 226 TYR 0.017 0.002 TYR A 605 ARG 0.008 0.001 ARG A 92 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 190 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 193 average time/residue: 0.2321 time to fit residues: 56.2070 Evaluate side-chains 193 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 187 time to evaluate : 0.661 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0588 time to fit residues: 1.6143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 34 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 76 optimal weight: 0.5980 chunk 70 optimal weight: 0.5980 chunk 61 optimal weight: 0.5980 chunk 6 optimal weight: 0.0010 chunk 47 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 48 optimal weight: 0.3980 chunk 65 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6357 Z= 0.217 Angle : 0.812 12.674 8593 Z= 0.407 Chirality : 0.050 0.385 947 Planarity : 0.005 0.049 1089 Dihedral : 6.983 71.342 871 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.13 % Allowed : 14.90 % Favored : 84.97 % Rotamer: Outliers : 0.44 % Allowed : 30.31 % Favored : 69.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.29), residues: 765 helix: -0.37 (0.30), residues: 315 sheet: -1.73 (0.72), residues: 37 loop : -3.38 (0.28), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 220 HIS 0.004 0.001 HIS A 811 PHE 0.050 0.002 PHE A 871 TYR 0.018 0.002 TYR A 605 ARG 0.009 0.001 ARG A 92 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 189 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 191 average time/residue: 0.2276 time to fit residues: 54.7924 Evaluate side-chains 195 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 193 time to evaluate : 0.733 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0564 time to fit residues: 1.1188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 56 optimal weight: 0.9980 chunk 9 optimal weight: 0.0070 chunk 16 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 25 optimal weight: 0.4980 chunk 62 optimal weight: 0.0770 chunk 7 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.157720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.140472 restraints weight = 10317.257| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 3.58 r_work: 0.3740 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6357 Z= 0.217 Angle : 0.823 13.685 8593 Z= 0.411 Chirality : 0.049 0.376 947 Planarity : 0.005 0.046 1089 Dihedral : 6.974 71.334 871 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.13 % Allowed : 15.29 % Favored : 84.58 % Rotamer: Outliers : 0.15 % Allowed : 31.63 % Favored : 68.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.29), residues: 765 helix: -0.46 (0.30), residues: 314 sheet: -1.47 (0.75), residues: 37 loop : -3.34 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 220 HIS 0.004 0.001 HIS A 811 PHE 0.043 0.002 PHE A 871 TYR 0.018 0.002 TYR A 605 ARG 0.009 0.001 ARG A 92 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2020.24 seconds wall clock time: 37 minutes 9.75 seconds (2229.75 seconds total)