Starting phenix.real_space_refine on Sun Apr 27 04:48:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8teg_41185/04_2025/8teg_41185.cif Found real_map, /net/cci-nas-00/data/ceres_data/8teg_41185/04_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_41185/04_2025/8teg_41185.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8teg_41185/04_2025/8teg_41185.map" model { file = "/net/cci-nas-00/data/ceres_data/8teg_41185/04_2025/8teg_41185.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8teg_41185/04_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-5669/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: 4.38, per 1000 atoms: 0.97 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: 1.04 Conformation dependent library (CDL) restraints added in 541.1 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: 0.51 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: 1.32 Time building geometry restraints manager: 1.26 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: 4.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 16.780 Find NCS groups from input model: 0.050 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:13.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.850 ------------------------------------------------------------------------------- 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= 0.238 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 Details of bonding type rmsd hydrogen bonds : bond 0.11955 ( 277) hydrogen bonds : angle 5.42258 ( 795) covalent geometry : bond 0.00672 ( 4553) covalent geometry : angle 0.74249 ( 6186) *********************** 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 : 0.518 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: 2.1964 time to fit residues: 155.5385 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 : 0.555 ------------------------------------------------------------------------------- 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 = 43)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.101945 restraints weight = 4015.284| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 1.10 r_work: 0.2971 rms_B_bonded: 1.52 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= 0.123 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 Details of bonding type rmsd hydrogen bonds : bond 0.05169 ( 277) hydrogen bonds : angle 4.69515 ( 795) covalent geometry : bond 0.00236 ( 4553) covalent geometry : angle 0.55321 ( 6186) *********************** 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 : 0.521 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 73 average time/residue: 1.6865 time to fit residues: 126.7760 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 : 0.484 ------------------------------------------------------------------------------- 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: 0.0980 chunk 8 optimal weight: 0.6980 chunk 54 optimal weight: 0.3980 chunk 28 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.3415 r_free = 0.3415 target = 0.125867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.102026 restraints weight = 4001.348| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 1.09 r_work: 0.2972 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.0857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 4553 Z= 0.122 Angle : 0.514 7.483 6186 Z= 0.266 Chirality : 0.040 0.140 698 Planarity : 0.004 0.031 769 Dihedral : 4.467 40.338 605 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % 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: 2.27 (0.36), residues: 553 helix: 1.80 (0.27), residues: 379 sheet: -2.55 (1.30), residues: 10 loop : 1.33 (0.50), residues: 164 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 0.009 0.001 TYR A 495 ARG 0.003 0.000 ARG B 637 Details of bonding type rmsd hydrogen bonds : bond 0.05246 ( 277) hydrogen bonds : angle 4.61019 ( 795) covalent geometry : bond 0.00235 ( 4553) covalent geometry : angle 0.51432 ( 6186) *********************** 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 71 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.517 Fit side-chains REVERT: A 617 GLU cc_start: 0.5748 (OUTLIER) cc_final: 0.5361 (tt0) outliers start: 7 outliers final: 3 residues processed: 69 average time/residue: 1.5171 time to fit residues: 108.0769 Evaluate side-chains 67 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 0.535 ------------------------------------------------------------------------------- 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: 0.0870 chunk 3 optimal weight: 0.0770 chunk 31 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 overall best weight: 0.4916 ------------------------------------------------------------------------------- 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 = 0.3417 r_free = 0.3417 target = 0.126001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.102100 restraints weight = 4031.278| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.10 r_work: 0.2977 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.0917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 4553 Z= 0.121 Angle : 0.512 7.512 6186 Z= 0.264 Chirality : 0.040 0.140 698 Planarity : 0.004 0.033 769 Dihedral : 4.450 41.030 605 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % 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: 2.27 (0.36), residues: 553 helix: 1.80 (0.27), residues: 379 sheet: -2.82 (1.32), residues: 10 loop : 1.36 (0.50), residues: 164 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 298 TYR 0.009 0.001 TYR A 495 ARG 0.003 0.000 ARG B 637 Details of bonding type rmsd hydrogen bonds : bond 0.05192 ( 277) hydrogen bonds : angle 4.56565 ( 795) covalent geometry : bond 0.00233 ( 4553) covalent geometry : angle 0.51179 ( 6186) *********************** 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 70 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.526 Fit side-chains REVERT: A 617 GLU cc_start: 0.5741 (OUTLIER) cc_final: 0.5330 (tt0) outliers start: 6 outliers final: 2 residues processed: 69 average time/residue: 1.5034 time to fit residues: 107.1272 Evaluate side-chains 66 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 63 time to evaluate : 0.515 ------------------------------------------------------------------------------- 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 617 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 33 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 16 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3396 r_free = 0.3396 target = 0.124365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.100102 restraints weight = 4046.989| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 1.11 r_work: 0.2942 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 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 0.030 4553 Z= 0.138 Angle : 0.550 7.609 6186 Z= 0.285 Chirality : 0.042 0.146 698 Planarity : 0.004 0.035 769 Dihedral : 4.564 42.969 605 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.69 % Allowed : 9.92 % 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: 2.14 (0.36), residues: 553 helix: 1.70 (0.27), residues: 378 sheet: -2.89 (1.35), residues: 10 loop : 1.31 (0.50), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 131 HIS 0.003 0.001 HIS A 312 PHE 0.016 0.001 PHE A 534 TYR 0.011 0.001 TYR A 495 ARG 0.003 0.000 ARG B 637 Details of bonding type rmsd hydrogen bonds : bond 0.05854 ( 277) hydrogen bonds : angle 4.68526 ( 795) covalent geometry : bond 0.00279 ( 4553) covalent geometry : angle 0.55043 ( 6186) *********************** 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 : 0.487 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 71 average time/residue: 1.5197 time to fit residues: 111.2534 Evaluate side-chains 66 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 63 time to evaluate : 0.470 ------------------------------------------------------------------------------- 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: 0.0030 chunk 8 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 14 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 52 optimal weight: 0.0970 chunk 31 optimal weight: 0.5980 chunk 43 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 overall best weight: 0.4188 ------------------------------------------------------------------------------- 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 = 0.3423 r_free = 0.3423 target = 0.126468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.102579 restraints weight = 3992.301| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.09 r_work: 0.2974 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.1039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4553 Z= 0.117 Angle : 0.509 7.548 6186 Z= 0.261 Chirality : 0.040 0.141 698 Planarity : 0.004 0.033 769 Dihedral : 4.459 42.368 605 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.84 % Allowed : 10.13 % 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: 2.30 (0.36), residues: 553 helix: 1.79 (0.27), residues: 379 sheet: -2.94 (1.34), residues: 10 loop : 1.48 (0.51), residues: 164 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 0.015 0.001 PHE A 298 TYR 0.008 0.001 TYR A 495 ARG 0.004 0.000 ARG B 637 Details of bonding type rmsd hydrogen bonds : bond 0.04981 ( 277) hydrogen bonds : angle 4.50550 ( 795) covalent geometry : bond 0.00227 ( 4553) covalent geometry : angle 0.50880 ( 6186) *********************** 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 66 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.527 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 66 average time/residue: 1.5191 time to fit residues: 103.5467 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 : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 LEU 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: 1.9990 chunk 25 optimal weight: 0.0010 chunk 21 optimal weight: 2.9990 chunk 43 optimal weight: 0.1980 chunk 48 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 31 optimal weight: 0.0980 chunk 13 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 overall best weight: 0.3586 ------------------------------------------------------------------------------- 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 = 0.3435 r_free = 0.3435 target = 0.127371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.103547 restraints weight = 4008.356| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 1.09 r_work: 0.2992 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.1156 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= 0.114 Angle : 0.504 7.400 6186 Z= 0.257 Chirality : 0.040 0.138 698 Planarity : 0.004 0.033 769 Dihedral : 4.392 42.391 605 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.63 % Allowed : 10.76 % 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: 2.39 (0.36), residues: 553 helix: 1.86 (0.27), residues: 379 sheet: -2.92 (1.33), residues: 10 loop : 1.52 (0.51), 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 0.008 0.001 TYR A 495 ARG 0.004 0.000 ARG B 637 Details of bonding type rmsd hydrogen bonds : bond 0.04780 ( 277) hydrogen bonds : angle 4.44290 ( 795) covalent geometry : bond 0.00218 ( 4553) covalent geometry : angle 0.50400 ( 6186) *********************** 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 65 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 62 time to evaluate : 0.476 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 64 average time/residue: 1.4751 time to fit residues: 97.5174 Evaluate side-chains 63 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 61 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0270 chunk 35 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 25 optimal weight: 0.0270 chunk 6 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 overall best weight: 0.4096 ------------------------------------------------------------------------------- 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 = 0.3431 r_free = 0.3431 target = 0.127051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.103142 restraints weight = 4046.269| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 1.10 r_work: 0.2974 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.1149 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= 0.116 Angle : 0.511 7.421 6186 Z= 0.260 Chirality : 0.040 0.138 698 Planarity : 0.004 0.033 769 Dihedral : 4.379 42.456 605 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.84 % Allowed : 10.34 % 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: 2.41 (0.36), residues: 553 helix: 1.87 (0.27), residues: 379 sheet: -2.91 (1.33), residues: 10 loop : 1.54 (0.51), 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 0.015 0.001 PHE A 298 TYR 0.009 0.001 TYR A 495 ARG 0.004 0.000 ARG B 637 Details of bonding type rmsd hydrogen bonds : bond 0.04888 ( 277) hydrogen bonds : angle 4.43817 ( 795) covalent geometry : bond 0.00225 ( 4553) covalent geometry : angle 0.51133 ( 6186) *********************** 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 66 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.520 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 66 average time/residue: 1.5345 time to fit residues: 104.5075 Evaluate side-chains 62 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 60 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 463 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 47 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 28 optimal weight: 0.0770 chunk 5 optimal weight: 4.9990 chunk 8 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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 = 0.3419 r_free = 0.3419 target = 0.126157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.102053 restraints weight = 4044.036| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 1.11 r_work: 0.2960 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.1109 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= 0.122 Angle : 0.523 7.519 6186 Z= 0.267 Chirality : 0.040 0.142 698 Planarity : 0.004 0.033 769 Dihedral : 4.425 43.040 605 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.42 % Allowed : 10.97 % 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: 2.34 (0.36), residues: 553 helix: 1.81 (0.27), residues: 379 sheet: -2.87 (1.33), residues: 10 loop : 1.51 (0.50), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 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 Details of bonding type rmsd hydrogen bonds : bond 0.05186 ( 277) hydrogen bonds : angle 4.49634 ( 795) covalent geometry : bond 0.00239 ( 4553) covalent geometry : angle 0.52323 ( 6186) *********************** 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 62 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 60 time to evaluate : 0.513 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 62 average time/residue: 1.6292 time to fit residues: 104.1684 Evaluate side-chains 62 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 60 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 463 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 51 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.124952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.100787 restraints weight = 3984.229| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 1.10 r_work: 0.2942 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.1036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4553 Z= 0.133 Angle : 0.551 7.638 6186 Z= 0.282 Chirality : 0.041 0.149 698 Planarity : 0.004 0.034 769 Dihedral : 4.517 43.586 605 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.42 % Allowed : 11.18 % 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: 2.20 (0.36), residues: 553 helix: 1.66 (0.27), residues: 384 sheet: -2.87 (1.34), residues: 10 loop : 1.56 (0.51), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 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 0.004 0.000 ARG B 637 Details of bonding type rmsd hydrogen bonds : bond 0.05636 ( 277) hydrogen bonds : angle 4.59226 ( 795) covalent geometry : bond 0.00266 ( 4553) covalent geometry : angle 0.55147 ( 6186) ********************** 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 64 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.532 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 64 average time/residue: 1.6061 time to fit residues: 106.1362 Evaluate side-chains 63 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 61 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 463 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 10 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.3383 r_free = 0.3383 target = 0.123460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.099139 restraints weight = 4001.991| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 1.10 r_work: 0.2922 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.0966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4553 Z= 0.156 Angle : 0.598 7.695 6186 Z= 0.308 Chirality : 0.044 0.158 698 Planarity : 0.005 0.035 769 Dihedral : 4.687 44.947 605 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 0.42 % Allowed : 11.39 % Favored : 88.19 % 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: 1.97 (0.36), residues: 553 helix: 1.51 (0.27), residues: 384 sheet: -2.84 (1.35), residues: 10 loop : 1.41 (0.51), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 247 HIS 0.003 0.001 HIS A 312 PHE 0.017 0.002 PHE A 534 TYR 0.013 0.002 TYR A 495 ARG 0.004 0.000 ARG A 222 Details of bonding type rmsd hydrogen bonds : bond 0.06377 ( 277) hydrogen bonds : angle 4.77440 ( 795) covalent geometry : bond 0.00326 ( 4553) covalent geometry : angle 0.59776 ( 6186) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4934.52 seconds wall clock time: 84 minutes 42.44 seconds (5082.44 seconds total)