Starting phenix.real_space_refine on Tue Feb 11 06:55:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8teg_41185/02_2025/8teg_41185.cif Found real_map, /net/cci-nas-00/data/ceres_data/8teg_41185/02_2025/8teg_41185.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8teg_41185/02_2025/8teg_41185.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8teg_41185/02_2025/8teg_41185.map" model { file = "/net/cci-nas-00/data/ceres_data/8teg_41185/02_2025/8teg_41185.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8teg_41185/02_2025/8teg_41185.cif" } resolution = 2.15 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 2926 2.51 5 N 716 2.21 5 O 846 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 4518 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4247 Classifications: {'peptide': 539} Link IDs: {'PCIS': 2, 'PTRANS': 33, 'TRANS': 503} Chain breaks: 2 Chain: "B" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 183 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 1, 'TRANS': 20} Chain: "A" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 81 Classifications: {'water': 81} Link IDs: {None: 80} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Time building chain proxies: 3.99, per 1000 atoms: 0.88 Number of scatterers: 4518 At special positions: 0 Unit cell: (73.87, 90.47, 84.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 30 16.00 O 846 8.00 N 716 7.00 C 2926 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: 1.22 Conformation dependent library (CDL) restraints added in 552.4 milliseconds 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1036 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 3 sheets defined 76.6% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 8 through 20 removed outlier: 3.772A pdb=" N MET A 20 " --> pdb=" O LYS A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 31 removed outlier: 4.057A pdb=" N GLY A 29 " --> pdb=" O ASP A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 35 removed outlier: 3.776A pdb=" N ARG A 35 " --> pdb=" O ALA A 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 32 through 35' Processing helix chain 'A' and resid 36 through 62 removed outlier: 3.610A pdb=" N ILE A 49 " --> pdb=" O PHE A 45 " (cutoff:3.500A) Proline residue: A 50 - end of helix Processing helix chain 'A' and resid 67 through 86 Processing helix chain 'A' and resid 96 through 112 removed outlier: 3.539A pdb=" N ALA A 112 " --> pdb=" O ASN A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 142 Processing helix chain 'A' and resid 143 through 151 removed outlier: 3.521A pdb=" N ILE A 147 " --> pdb=" O ALA A 144 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE A 148 " --> pdb=" O CYS A 145 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ASN A 149 " --> pdb=" O SER A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 178 removed outlier: 3.517A pdb=" N LEU A 158 " --> pdb=" O VAL A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 192 Processing helix chain 'A' and resid 193 through 219 removed outlier: 3.542A pdb=" N ARG A 219 " --> pdb=" O GLY A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 224 Processing helix chain 'A' and resid 228 through 252 removed outlier: 6.235A pdb=" N VAL A 240 " --> pdb=" O ALA A 236 " (cutoff:3.500A) Proline residue: A 241 - end of helix Processing helix chain 'A' and resid 253 through 258 removed outlier: 4.572A pdb=" N GLY A 256 " --> pdb=" O ILE A 253 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL A 258 " --> pdb=" O ALA A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 287 Processing helix chain 'A' and resid 290 through 297 Processing helix chain 'A' and resid 297 through 320 removed outlier: 3.615A pdb=" N MET A 303 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER A 313 " --> pdb=" O TYR A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 325 Processing helix chain 'A' and resid 331 through 350 Processing helix chain 'A' and resid 359 through 368 Processing helix chain 'A' and resid 464 through 480 removed outlier: 3.924A pdb=" N VAL A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ALA A 479 " --> pdb=" O GLY A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 485 Processing helix chain 'A' and resid 488 through 503 removed outlier: 3.696A pdb=" N LEU A 492 " --> pdb=" O PRO A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 517 Processing helix chain 'A' and resid 519 through 521 No H-bonds generated for 'chain 'A' and resid 519 through 521' Processing helix chain 'A' and resid 522 through 528 removed outlier: 3.923A pdb=" N VAL A 526 " --> pdb=" O ARG A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 538 Processing helix chain 'A' and resid 539 through 561 Processing helix chain 'A' and resid 565 through 568 Processing helix chain 'A' and resid 569 through 584 removed outlier: 3.526A pdb=" N MET A 573 " --> pdb=" O MET A 569 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU A 577 " --> pdb=" O MET A 573 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ILE A 578 " --> pdb=" O ILE A 574 " (cutoff:3.500A) Proline residue: A 579 - end of helix Processing helix chain 'A' and resid 584 through 589 removed outlier: 3.709A pdb=" N PHE A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 598 Processing helix chain 'A' and resid 609 through 614 Processing helix chain 'B' and resid 626 through 635 removed outlier: 3.731A pdb=" N GLU B 633 " --> pdb=" O GLU B 629 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 93 through 94 Processing sheet with id=AA2, first strand: chain 'A' and resid 369 through 371 Processing sheet with id=AA3, first strand: chain 'A' and resid 531 through 532 277 hydrogen bonds defined for protein. 795 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: 1.27 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.10 - 1.24: 568 1.24 - 1.38: 1174 1.38 - 1.53: 2133 1.53 - 1.67: 626 1.67 - 1.81: 52 Bond restraints: 4553 Sorted by residual: bond pdb=" CG PRO A 114 " pdb=" CD PRO A 114 " ideal model delta sigma weight residual 1.503 1.099 0.404 3.40e-02 8.65e+02 1.41e+02 bond pdb=" N PRO A 114 " pdb=" CA PRO A 114 " ideal model delta sigma weight residual 1.471 1.521 -0.050 1.32e-02 5.74e+03 1.42e+01 bond pdb=" N PRO A 114 " pdb=" CD PRO A 114 " ideal model delta sigma weight residual 1.473 1.515 -0.042 1.40e-02 5.10e+03 8.90e+00 bond pdb=" CA PRO A 114 " pdb=" CB PRO A 114 " ideal model delta sigma weight residual 1.534 1.509 0.025 1.43e-02 4.89e+03 3.05e+00 bond pdb=" N PHE A 5 " pdb=" CA PHE A 5 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.96e+00 ... (remaining 4548 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.01: 6179 5.01 - 10.02: 5 10.02 - 15.02: 0 15.02 - 20.03: 0 20.03 - 25.04: 2 Bond angle restraints: 6186 Sorted by residual: angle pdb=" N PRO A 114 " pdb=" CD PRO A 114 " pdb=" CG PRO A 114 " ideal model delta sigma weight residual 103.20 78.16 25.04 1.50e+00 4.44e-01 2.79e+02 angle pdb=" CA PRO A 114 " pdb=" CB PRO A 114 " pdb=" CG PRO A 114 " ideal model delta sigma weight residual 104.50 79.68 24.82 1.90e+00 2.77e-01 1.71e+02 angle pdb=" N PRO A 114 " pdb=" CA PRO A 114 " pdb=" CB PRO A 114 " ideal model delta sigma weight residual 103.30 97.17 6.13 1.12e+00 7.97e-01 3.00e+01 angle pdb=" CA PRO A 114 " pdb=" N PRO A 114 " pdb=" CD PRO A 114 " ideal model delta sigma weight residual 112.00 105.20 6.80 1.40e+00 5.10e-01 2.36e+01 angle pdb=" N LEU A 504 " pdb=" CA LEU A 504 " pdb=" C LEU A 504 " ideal model delta sigma weight residual 109.81 116.27 -6.46 2.21e+00 2.05e-01 8.54e+00 ... (remaining 6181 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 2360 17.69 - 35.39: 245 35.39 - 53.08: 52 53.08 - 70.78: 9 70.78 - 88.47: 8 Dihedral angle restraints: 2674 sinusoidal: 1062 harmonic: 1612 Sorted by residual: dihedral pdb=" CA LYS A 590 " pdb=" C LYS A 590 " pdb=" N GLY A 591 " pdb=" CA GLY A 591 " ideal model delta harmonic sigma weight residual 180.00 157.04 22.96 0 5.00e+00 4.00e-02 2.11e+01 dihedral pdb=" N PRO A 114 " pdb=" CG PRO A 114 " pdb=" CD PRO A 114 " pdb=" CB PRO A 114 " ideal model delta sinusoidal sigma weight residual 30.00 81.50 -51.50 1 1.50e+01 4.44e-03 1.61e+01 dihedral pdb=" CA LEU A 504 " pdb=" C LEU A 504 " pdb=" N PRO A 505 " pdb=" CA PRO A 505 " ideal model delta harmonic sigma weight residual -180.00 -160.62 -19.38 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 2671 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 444 0.030 - 0.060: 173 0.060 - 0.090: 51 0.090 - 0.120: 23 0.120 - 0.150: 7 Chirality restraints: 698 Sorted by residual: chirality pdb=" CA ILE A 358 " pdb=" N ILE A 358 " pdb=" C ILE A 358 " pdb=" CB ILE A 358 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.64e-01 chirality pdb=" CA PRO A 505 " pdb=" N PRO A 505 " pdb=" C PRO A 505 " pdb=" CB PRO A 505 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.31e-01 chirality pdb=" CA PRO A 564 " pdb=" N PRO A 564 " pdb=" C PRO A 564 " pdb=" CB PRO A 564 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.31e-01 ... (remaining 695 not shown) Planarity restraints: 769 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 580 " 0.006 2.00e-02 2.50e+03 1.17e-02 1.37e+00 pdb=" C VAL A 580 " -0.020 2.00e-02 2.50e+03 pdb=" O VAL A 580 " 0.008 2.00e-02 2.50e+03 pdb=" N ARG A 581 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 97 " -0.018 5.00e-02 4.00e+02 2.75e-02 1.21e+00 pdb=" N PRO A 98 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO A 98 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 98 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 253 " -0.016 5.00e-02 4.00e+02 2.47e-02 9.76e-01 pdb=" N PRO A 254 " 0.043 5.00e-02 4.00e+02 pdb=" CA PRO A 254 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 254 " -0.014 5.00e-02 4.00e+02 ... (remaining 766 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 226 2.73 - 3.27: 4804 3.27 - 3.81: 7945 3.81 - 4.36: 9877 4.36 - 4.90: 15723 Nonbonded interactions: 38575 Sorted by model distance: nonbonded pdb=" O ALA A 144 " pdb=" OH TYR A 309 " model vdw 2.185 3.040 nonbonded pdb=" OD1 ASP A 25 " pdb=" NZ LYS A 328 " model vdw 2.317 3.120 nonbonded pdb=" N GLU A 323 " pdb=" OE1 GLU A 323 " model vdw 2.414 3.120 nonbonded pdb=" OD2 ASP A 335 " pdb=" O HOH A 801 " model vdw 2.419 3.040 nonbonded pdb=" O LYS A 260 " pdb=" O HOH A 802 " model vdw 2.442 3.040 ... (remaining 38570 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.930 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 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 : 0.007 0.404 4553 Z= 0.348 Angle : 0.742 25.041 6186 Z= 0.415 Chirality : 0.039 0.150 698 Planarity : 0.004 0.027 769 Dihedral : 15.683 88.472 1638 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.05 % Allowed : 9.28 % Favored : 89.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.36), residues: 553 helix: 1.36 (0.27), residues: 384 sheet: -1.48 (1.36), residues: 10 loop : 1.33 (0.50), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 247 HIS 0.003 0.001 HIS A 312 PHE 0.012 0.001 PHE A 534 TYR 0.013 0.001 TYR A 495 ARG 0.004 0.000 ARG A 222 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.487 Fit side-chains REVERT: A 114 PRO cc_start: 0.7985 (Cg_exo) cc_final: 0.7612 (Cg_exo) REVERT: B 629 GLU cc_start: 0.8387 (tt0) cc_final: 0.8178 (tt0) outliers start: 5 outliers final: 3 residues processed: 69 average time/residue: 1.8037 time to fit residues: 128.1018 Evaluate side-chains 67 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 64 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 462 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 46 optimal weight: 0.8980 chunk 41 optimal weight: 0.2980 chunk 23 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 43 optimal weight: 0.0670 chunk 16 optimal weight: 2.9990 chunk 26 optimal weight: 0.0070 chunk 32 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 overall best weight: 0.3736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.126008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.101951 restraints weight = 4015.243| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 1.10 r_work: 0.2971 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 2.48 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.0711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 4553 Z= 0.148 Angle : 0.553 10.184 6186 Z= 0.283 Chirality : 0.040 0.143 698 Planarity : 0.004 0.029 769 Dihedral : 4.856 37.653 612 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.05 % Allowed : 9.07 % Favored : 89.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 2.25 (0.36), residues: 553 helix: 1.81 (0.27), residues: 377 sheet: -2.44 (1.28), residues: 10 loop : 1.25 (0.50), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 247 HIS 0.003 0.001 HIS A 312 PHE 0.020 0.001 PHE A 298 TYR 0.007 0.001 TYR A 495 ARG 0.003 0.000 ARG B 637 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.547 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 73 average time/residue: 1.6781 time to fit residues: 126.1820 Evaluate side-chains 67 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 64 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 463 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 45 optimal weight: 5.9990 chunk 37 optimal weight: 0.3980 chunk 22 optimal weight: 0.7980 chunk 26 optimal weight: 0.0470 chunk 8 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN A 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.125130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.101162 restraints weight = 3992.536| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 1.09 r_work: 0.2966 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 2.48 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.0804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4553 Z= 0.158 Angle : 0.527 7.543 6186 Z= 0.273 Chirality : 0.041 0.142 698 Planarity : 0.004 0.032 769 Dihedral : 4.505 40.706 605 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.48 % Allowed : 9.49 % Favored : 89.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 2.22 (0.36), residues: 553 helix: 1.77 (0.27), residues: 378 sheet: -2.53 (1.31), residues: 10 loop : 1.29 (0.49), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 247 HIS 0.003 0.001 HIS A 312 PHE 0.016 0.001 PHE A 298 TYR 0.010 0.001 TYR A 495 ARG 0.003 0.000 ARG B 637 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.531 Fit side-chains REVERT: A 617 GLU cc_start: 0.5836 (OUTLIER) cc_final: 0.5424 (tt0) outliers start: 7 outliers final: 3 residues processed: 70 average time/residue: 1.6176 time to fit residues: 116.7422 Evaluate side-chains 68 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 64 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 617 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 43 optimal weight: 0.9980 chunk 3 optimal weight: 0.4980 chunk 31 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.2980 chunk 28 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.125211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.101175 restraints weight = 4018.752| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 1.09 r_work: 0.2966 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.0867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4553 Z= 0.157 Angle : 0.525 7.595 6186 Z= 0.272 Chirality : 0.041 0.144 698 Planarity : 0.004 0.033 769 Dihedral : 4.519 42.162 605 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.27 % Allowed : 10.13 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 2.19 (0.36), residues: 553 helix: 1.75 (0.27), residues: 378 sheet: -2.79 (1.33), residues: 10 loop : 1.30 (0.49), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 247 HIS 0.003 0.001 HIS A 312 PHE 0.015 0.001 PHE A 534 TYR 0.010 0.001 TYR A 495 ARG 0.003 0.000 ARG B 637 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.541 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 69 average time/residue: 1.5628 time to fit residues: 111.2889 Evaluate side-chains 64 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 292 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 33 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 37 optimal weight: 0.4980 chunk 16 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.122637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.098247 restraints weight = 4042.161| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 1.11 r_work: 0.2919 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 2.49 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.0859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4553 Z= 0.226 Angle : 0.604 7.740 6186 Z= 0.316 Chirality : 0.044 0.158 698 Planarity : 0.005 0.037 769 Dihedral : 4.741 45.072 605 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.69 % Allowed : 9.70 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.36), residues: 553 helix: 1.44 (0.27), residues: 384 sheet: -2.81 (1.37), residues: 10 loop : 1.33 (0.50), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 131 HIS 0.003 0.001 HIS A 312 PHE 0.017 0.002 PHE A 534 TYR 0.014 0.002 TYR A 495 ARG 0.005 0.001 ARG A 222 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.509 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 71 average time/residue: 1.5985 time to fit residues: 117.1377 Evaluate side-chains 67 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 64 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 463 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 26 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.123716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.099486 restraints weight = 3967.991| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 1.10 r_work: 0.2920 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.0900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4553 Z= 0.183 Angle : 0.560 7.788 6186 Z= 0.292 Chirality : 0.042 0.150 698 Planarity : 0.004 0.036 769 Dihedral : 4.680 44.001 605 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.27 % Allowed : 9.49 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.36), residues: 553 helix: 1.59 (0.27), residues: 378 sheet: -2.85 (1.38), residues: 10 loop : 1.23 (0.49), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 247 HIS 0.003 0.001 HIS A 312 PHE 0.016 0.001 PHE A 298 TYR 0.011 0.001 TYR A 495 ARG 0.003 0.000 ARG A 222 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.400 Fit side-chains REVERT: A 23 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7908 (tttm) outliers start: 6 outliers final: 4 residues processed: 66 average time/residue: 1.6213 time to fit residues: 110.3174 Evaluate side-chains 68 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 463 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 20 optimal weight: 0.8980 chunk 25 optimal weight: 0.0470 chunk 21 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 31 optimal weight: 0.0970 chunk 13 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 overall best weight: 0.4676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.125544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.101472 restraints weight = 3990.073| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 1.10 r_work: 0.2960 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 2.49 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.1047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4553 Z= 0.148 Angle : 0.521 7.543 6186 Z= 0.268 Chirality : 0.040 0.144 698 Planarity : 0.004 0.033 769 Dihedral : 4.515 42.470 605 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.48 % Allowed : 9.92 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 2.22 (0.36), residues: 553 helix: 1.76 (0.27), residues: 378 sheet: -2.88 (1.37), residues: 10 loop : 1.35 (0.50), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 247 HIS 0.002 0.001 HIS A 312 PHE 0.015 0.001 PHE A 298 TYR 0.009 0.001 TYR A 495 ARG 0.004 0.000 ARG B 637 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.578 Fit side-chains REVERT: A 23 LYS cc_start: 0.8075 (OUTLIER) cc_final: 0.7825 (tttm) REVERT: A 257 ASP cc_start: 0.7249 (OUTLIER) cc_final: 0.6922 (m-30) outliers start: 7 outliers final: 2 residues processed: 70 average time/residue: 1.6327 time to fit residues: 117.8725 Evaluate side-chains 68 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 64 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 463 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 52 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 51 optimal weight: 20.0000 chunk 29 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 25 optimal weight: 0.3980 chunk 6 optimal weight: 0.0570 chunk 11 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.125470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.101413 restraints weight = 4021.237| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 1.10 r_work: 0.2955 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 4553 Z= 0.155 Angle : 0.531 7.571 6186 Z= 0.273 Chirality : 0.040 0.142 698 Planarity : 0.004 0.035 769 Dihedral : 4.503 43.010 605 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.27 % Allowed : 10.34 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 2.22 (0.36), residues: 553 helix: 1.75 (0.27), residues: 379 sheet: -2.84 (1.38), residues: 10 loop : 1.39 (0.50), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 247 HIS 0.002 0.001 HIS A 312 PHE 0.016 0.001 PHE A 298 TYR 0.010 0.001 TYR A 495 ARG 0.004 0.000 ARG B 637 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.533 Fit side-chains REVERT: A 23 LYS cc_start: 0.8080 (OUTLIER) cc_final: 0.7830 (tttm) REVERT: A 257 ASP cc_start: 0.7233 (OUTLIER) cc_final: 0.6923 (m-30) REVERT: A 502 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.8347 (mt-10) outliers start: 6 outliers final: 2 residues processed: 69 average time/residue: 1.6623 time to fit residues: 118.1733 Evaluate side-chains 68 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 502 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 47 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 28 optimal weight: 0.0040 chunk 5 optimal weight: 5.9990 chunk 8 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.124283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.100030 restraints weight = 4019.092| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 1.10 r_work: 0.2932 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.0967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4553 Z= 0.175 Angle : 0.556 7.654 6186 Z= 0.287 Chirality : 0.042 0.147 698 Planarity : 0.004 0.036 769 Dihedral : 4.581 43.538 605 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.27 % Allowed : 9.92 % Favored : 88.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 2.08 (0.36), residues: 553 helix: 1.60 (0.27), residues: 384 sheet: -2.82 (1.39), residues: 10 loop : 1.44 (0.51), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 247 HIS 0.002 0.001 HIS A 312 PHE 0.017 0.001 PHE A 298 TYR 0.011 0.001 TYR A 495 ARG 0.003 0.000 ARG B 637 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.624 Fit side-chains REVERT: A 23 LYS cc_start: 0.8118 (OUTLIER) cc_final: 0.7871 (tttm) REVERT: A 257 ASP cc_start: 0.7271 (OUTLIER) cc_final: 0.6955 (m-30) REVERT: A 502 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8369 (mt-10) outliers start: 6 outliers final: 3 residues processed: 67 average time/residue: 1.6825 time to fit residues: 116.3529 Evaluate side-chains 68 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 568 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 51 optimal weight: 20.0000 chunk 26 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 48 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.124035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.099808 restraints weight = 3972.272| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.10 r_work: 0.2930 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.0958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4553 Z= 0.181 Angle : 0.570 7.688 6186 Z= 0.293 Chirality : 0.042 0.149 698 Planarity : 0.004 0.036 769 Dihedral : 4.616 43.698 605 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.27 % Allowed : 10.13 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 2.03 (0.36), residues: 553 helix: 1.56 (0.27), residues: 384 sheet: -2.81 (1.38), residues: 10 loop : 1.40 (0.51), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 247 HIS 0.003 0.001 HIS A 312 PHE 0.017 0.001 PHE A 298 TYR 0.011 0.001 TYR A 495 ARG 0.003 0.000 ARG B 637 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.503 Fit side-chains REVERT: A 23 LYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7896 (tttm) REVERT: A 257 ASP cc_start: 0.7288 (OUTLIER) cc_final: 0.6965 (m-30) REVERT: A 502 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.8375 (mt-10) outliers start: 6 outliers final: 3 residues processed: 67 average time/residue: 1.6495 time to fit residues: 113.8916 Evaluate side-chains 67 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 568 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 10 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 6 optimal weight: 0.0980 chunk 24 optimal weight: 0.1980 chunk 36 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.124993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.100892 restraints weight = 3993.631| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 1.10 r_work: 0.2947 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.1008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4553 Z= 0.162 Angle : 0.551 7.948 6186 Z= 0.282 Chirality : 0.041 0.145 698 Planarity : 0.004 0.035 769 Dihedral : 4.552 42.989 605 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.48 % Allowed : 10.13 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 2.13 (0.36), residues: 553 helix: 1.63 (0.27), residues: 384 sheet: -2.80 (1.38), residues: 10 loop : 1.48 (0.51), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 247 HIS 0.002 0.001 HIS A 312 PHE 0.017 0.001 PHE A 298 TYR 0.010 0.001 TYR A 293 ARG 0.003 0.000 ARG B 637 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4809.90 seconds wall clock time: 85 minutes 10.52 seconds (5110.52 seconds total)