Starting phenix.real_space_refine on Thu Jul 31 01:51:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ugb_64135/07_2025/9ugb_64135.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ugb_64135/07_2025/9ugb_64135.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ugb_64135/07_2025/9ugb_64135.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ugb_64135/07_2025/9ugb_64135.map" model { file = "/net/cci-nas-00/data/ceres_data/9ugb_64135/07_2025/9ugb_64135.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ugb_64135/07_2025/9ugb_64135.cif" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.047 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: 5 Type Number sf(0) Gaussians S 29 5.16 5 C 4144 2.51 5 N 1062 2.21 5 O 1198 1.98 5 H 6509 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12942 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 12670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 821, 12670 Classifications: {'peptide': 821} Link IDs: {'PTRANS': 33, 'TRANS': 787} Chain: "C" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 272 Classifications: {'peptide': 19} Link IDs: {'TRANS': 18} Time building chain proxies: 7.30, per 1000 atoms: 0.56 Number of scatterers: 12942 At special positions: 0 Unit cell: (82.16, 87.36, 132.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 29 16.00 O 1198 8.00 N 1062 7.00 C 4144 6.00 H 6509 1.00 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: 3.41 Conformation dependent library (CDL) restraints added in 1.1 seconds 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1532 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 5 sheets defined 59.6% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'B' and resid 76 through 80 Processing helix chain 'B' and resid 89 through 101 Processing helix chain 'B' and resid 111 through 121 removed outlier: 3.902A pdb=" N PHE B 120 " --> pdb=" O PHE B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 138 Processing helix chain 'B' and resid 140 through 172 removed outlier: 3.541A pdb=" N ILE B 168 " --> pdb=" O GLN B 164 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL B 169 " --> pdb=" O ALA B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 196 No H-bonds generated for 'chain 'B' and resid 194 through 196' Processing helix chain 'B' and resid 227 through 232 Processing helix chain 'B' and resid 263 through 266 Processing helix chain 'B' and resid 267 through 280 Processing helix chain 'B' and resid 284 through 315 Processing helix chain 'B' and resid 318 through 334 Processing helix chain 'B' and resid 337 through 356 Processing helix chain 'B' and resid 363 through 371 removed outlier: 4.044A pdb=" N GLU B 367 " --> pdb=" O LEU B 363 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY B 371 " --> pdb=" O GLU B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 411 Processing helix chain 'B' and resid 420 through 430 Processing helix chain 'B' and resid 433 through 441 removed outlier: 4.093A pdb=" N THR B 441 " --> pdb=" O LYS B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 488 removed outlier: 3.772A pdb=" N ASP B 487 " --> pdb=" O THR B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 508 Processing helix chain 'B' and resid 540 through 550 removed outlier: 3.524A pdb=" N GLU B 546 " --> pdb=" O GLN B 542 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA B 547 " --> pdb=" O THR B 543 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG B 548 " --> pdb=" O VAL B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 573 Processing helix chain 'B' and resid 581 through 585 Processing helix chain 'B' and resid 593 through 604 Processing helix chain 'B' and resid 611 through 625 Processing helix chain 'B' and resid 638 through 645 Processing helix chain 'B' and resid 655 through 662 Processing helix chain 'B' and resid 673 through 714 Processing helix chain 'B' and resid 718 through 734 Processing helix chain 'B' and resid 735 through 739 Processing helix chain 'B' and resid 751 through 776 Processing helix chain 'B' and resid 790 through 811 removed outlier: 4.062A pdb=" N ILE B 807 " --> pdb=" O GLU B 803 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N PHE B 808 " --> pdb=" O ASN B 804 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE B 809 " --> pdb=" O TRP B 805 " (cutoff:3.500A) Processing helix chain 'B' and resid 822 through 842 Processing helix chain 'B' and resid 851 through 879 Processing helix chain 'B' and resid 879 through 888 Processing helix chain 'C' and resid 42 through 51 removed outlier: 3.818A pdb=" N LEU C 46 " --> pdb=" O ASP C 42 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLN C 51 " --> pdb=" O ILE C 47 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 187 through 192 removed outlier: 5.138A pdb=" N VAL B 181 " --> pdb=" O GLN B 203 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ILE B 201 " --> pdb=" O ILE B 183 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 237 through 239 removed outlier: 6.504A pdb=" N GLN B 224 " --> pdb=" O LYS B 252 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 358 through 360 removed outlier: 6.254A pdb=" N GLY B 648 " --> pdb=" O ILE B 664 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N PHE B 666 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ALA B 650 " --> pdb=" O PHE B 666 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N VAL B 629 " --> pdb=" O THR B 647 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ILE B 649 " --> pdb=" O VAL B 629 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N MET B 631 " --> pdb=" O ILE B 649 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU B 628 " --> pdb=" O VAL B 372 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N GLU B 373 " --> pdb=" O ARG B 553 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N LYS B 555 " --> pdb=" O GLU B 373 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LEU B 375 " --> pdb=" O LYS B 555 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N LEU B 557 " --> pdb=" O LEU B 375 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N SER B 377 " --> pdb=" O LEU B 557 " (cutoff:3.500A) removed outlier: 8.683A pdb=" N PHE B 607 " --> pdb=" O VAL B 554 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N MET B 556 " --> pdb=" O PHE B 607 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 389 through 390 Processing sheet with id=AA5, first strand: chain 'B' and resid 394 through 395 removed outlier: 6.742A pdb=" N VAL B 515 " --> pdb=" O LEU B 527 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N LYS B 457 " --> pdb=" O PRO B 450 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N THR B 459 " --> pdb=" O PHE B 448 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N PHE B 448 " --> pdb=" O THR B 459 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL B 461 " --> pdb=" O LEU B 446 " (cutoff:3.500A) 408 hydrogen bonds defined for protein. 1179 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: 5.33 Time building geometry restraints manager: 4.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6500 1.03 - 1.23: 15 1.23 - 1.42: 2664 1.42 - 1.62: 3845 1.62 - 1.81: 49 Bond restraints: 13073 Sorted by residual: bond pdb=" CA THR B 384 " pdb=" HA THR B 384 " ideal model delta sigma weight residual 0.970 0.855 0.115 2.00e-02 2.50e+03 3.28e+01 bond pdb=" N GLY B 284 " pdb=" CA GLY B 284 " ideal model delta sigma weight residual 1.444 1.477 -0.033 1.06e-02 8.90e+03 9.69e+00 bond pdb=" N GLN B 283 " pdb=" CA GLN B 283 " ideal model delta sigma weight residual 1.453 1.489 -0.036 1.31e-02 5.83e+03 7.43e+00 bond pdb=" N MET B 533 " pdb=" H MET B 533 " ideal model delta sigma weight residual 0.860 0.911 -0.051 2.00e-02 2.50e+03 6.59e+00 bond pdb=" N ASP B 378 " pdb=" H ASP B 378 " ideal model delta sigma weight residual 0.860 0.911 -0.051 2.00e-02 2.50e+03 6.52e+00 ... (remaining 13068 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.93: 23718 6.93 - 13.85: 3 13.85 - 20.78: 0 20.78 - 27.71: 0 27.71 - 34.64: 3 Bond angle restraints: 23724 Sorted by residual: angle pdb=" C LEU B 172 " pdb=" CA LEU B 172 " pdb=" HA LEU B 172 " ideal model delta sigma weight residual 109.00 74.36 34.64 3.00e+00 1.11e-01 1.33e+02 angle pdb=" N LEU B 172 " pdb=" CA LEU B 172 " pdb=" HA LEU B 172 " ideal model delta sigma weight residual 110.00 75.87 34.13 3.00e+00 1.11e-01 1.29e+02 angle pdb=" CB LEU B 172 " pdb=" CA LEU B 172 " pdb=" HA LEU B 172 " ideal model delta sigma weight residual 109.00 77.25 31.75 3.00e+00 1.11e-01 1.12e+02 angle pdb=" C GLY B 281 " pdb=" N GLY B 282 " pdb=" CA GLY B 282 " ideal model delta sigma weight residual 119.92 124.33 -4.41 9.60e-01 1.09e+00 2.11e+01 angle pdb=" CA GLY B 282 " pdb=" C GLY B 282 " pdb=" O GLY B 282 " ideal model delta sigma weight residual 121.41 117.54 3.87 8.80e-01 1.29e+00 1.93e+01 ... (remaining 23719 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.04: 5272 17.04 - 34.07: 542 34.07 - 51.11: 182 51.11 - 68.14: 91 68.14 - 85.18: 19 Dihedral angle restraints: 6106 sinusoidal: 3320 harmonic: 2786 Sorted by residual: dihedral pdb=" C LEU B 172 " pdb=" N LEU B 172 " pdb=" CA LEU B 172 " pdb=" CB LEU B 172 " ideal model delta harmonic sigma weight residual -122.60 -133.29 10.69 0 2.50e+00 1.60e-01 1.83e+01 dihedral pdb=" N LEU B 172 " pdb=" C LEU B 172 " pdb=" CA LEU B 172 " pdb=" CB LEU B 172 " ideal model delta harmonic sigma weight residual 122.80 133.42 -10.62 0 2.50e+00 1.60e-01 1.80e+01 dihedral pdb=" CA ASP C 40 " pdb=" C ASP C 40 " pdb=" N ASP C 41 " pdb=" CA ASP C 41 " ideal model delta harmonic sigma weight residual 180.00 -159.87 -20.13 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 6103 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 975 0.091 - 0.181: 64 0.181 - 0.272: 1 0.272 - 0.363: 1 0.363 - 0.453: 1 Chirality restraints: 1042 Sorted by residual: chirality pdb=" CA LEU B 172 " pdb=" N LEU B 172 " pdb=" C LEU B 172 " pdb=" CB LEU B 172 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.14e+00 chirality pdb=" CA THR B 384 " pdb=" N THR B 384 " pdb=" C THR B 384 " pdb=" CB THR B 384 " both_signs ideal model delta sigma weight residual False 2.53 2.22 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CA ILE B 820 " pdb=" N ILE B 820 " pdb=" C ILE B 820 " pdb=" CB ILE B 820 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 1039 not shown) Planarity restraints: 1938 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN B 623 " -0.254 2.00e-02 2.50e+03 3.19e-01 1.52e+03 pdb=" CD GLN B 623 " 0.030 2.00e-02 2.50e+03 pdb=" OE1 GLN B 623 " 0.239 2.00e-02 2.50e+03 pdb=" NE2 GLN B 623 " 0.005 2.00e-02 2.50e+03 pdb="HE21 GLN B 623 " -0.503 2.00e-02 2.50e+03 pdb="HE22 GLN B 623 " 0.483 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 384 " -0.020 2.00e-02 2.50e+03 3.90e-02 1.52e+01 pdb=" N LYS B 385 " 0.067 2.00e-02 2.50e+03 pdb=" CA LYS B 385 " -0.017 2.00e-02 2.50e+03 pdb=" H LYS B 385 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 822 " -0.015 2.00e-02 2.50e+03 2.97e-02 8.81e+00 pdb=" N TRP B 823 " 0.051 2.00e-02 2.50e+03 pdb=" CA TRP B 823 " -0.013 2.00e-02 2.50e+03 pdb=" H TRP B 823 " -0.023 2.00e-02 2.50e+03 ... (remaining 1935 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.08: 260 2.08 - 2.71: 22061 2.71 - 3.34: 39756 3.34 - 3.97: 48717 3.97 - 4.60: 77610 Nonbonded interactions: 188404 Sorted by model distance: nonbonded pdb=" OE1 GLU B 190 " pdb=" H GLU B 190 " model vdw 1.454 2.450 nonbonded pdb="HE22 GLN B 623 " pdb=" HA ALA B 645 " model vdw 1.530 2.270 nonbonded pdb=" OE1 GLN B 824 " pdb=" H GLN B 824 " model vdw 1.600 2.450 nonbonded pdb=" HE1 TRP B 805 " pdb=" OD2 ASP B 833 " model vdw 1.609 2.450 nonbonded pdb="HH21 ARG B 315 " pdb=" O ALA B 711 " model vdw 1.626 2.450 ... (remaining 188399 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: 2.580 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: 0.250 Extract box with map and model: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 33.120 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 6564 Z= 0.231 Angle : 0.721 8.686 8921 Z= 0.437 Chirality : 0.047 0.453 1042 Planarity : 0.005 0.064 1133 Dihedral : 15.663 84.083 2352 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.29 % Allowed : 16.20 % Favored : 83.50 % Cbeta Deviations : 0.26 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.28), residues: 836 helix: 1.47 (0.23), residues: 470 sheet: -0.98 (0.49), residues: 101 loop : -0.46 (0.36), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 141 HIS 0.007 0.001 HIS B 701 PHE 0.023 0.002 PHE B 126 TYR 0.016 0.001 TYR B 498 ARG 0.005 0.001 ARG B 324 Details of bonding type rmsd hydrogen bonds : bond 0.12046 ( 408) hydrogen bonds : angle 6.10535 ( 1179) covalent geometry : bond 0.00426 ( 6564) covalent geometry : angle 0.72122 ( 8921) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 106 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 405 MET cc_start: 0.7176 (mmt) cc_final: 0.6914 (mmt) outliers start: 2 outliers final: 1 residues processed: 106 average time/residue: 0.3523 time to fit residues: 51.5045 Evaluate side-chains 92 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 91 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 70 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 42 optimal weight: 0.0010 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 48 optimal weight: 0.4980 chunk 75 optimal weight: 0.8980 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 187 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.182822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.149303 restraints weight = 23504.545| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 2.05 r_work: 0.3592 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3465 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6564 Z= 0.158 Angle : 0.545 5.940 8921 Z= 0.287 Chirality : 0.043 0.414 1042 Planarity : 0.004 0.060 1133 Dihedral : 4.150 28.400 893 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.46 % Allowed : 15.62 % Favored : 82.92 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.27), residues: 836 helix: 1.69 (0.22), residues: 471 sheet: -1.41 (0.49), residues: 79 loop : -0.16 (0.34), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 141 HIS 0.005 0.001 HIS B 701 PHE 0.020 0.002 PHE B 126 TYR 0.011 0.001 TYR B 691 ARG 0.004 0.001 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.04119 ( 408) hydrogen bonds : angle 4.81776 ( 1179) covalent geometry : bond 0.00353 ( 6564) covalent geometry : angle 0.54530 ( 8921) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 405 MET cc_start: 0.7093 (mmt) cc_final: 0.6372 (mmt) REVERT: B 592 MET cc_start: 0.0738 (mtm) cc_final: 0.0509 (mtp) REVERT: B 714 ASP cc_start: 0.8485 (t0) cc_final: 0.8179 (t0) outliers start: 10 outliers final: 4 residues processed: 121 average time/residue: 0.2818 time to fit residues: 50.2710 Evaluate side-chains 97 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 93 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 846 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 38 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 53 optimal weight: 0.0980 chunk 68 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 391 HIS B 577 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.176358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.142496 restraints weight = 23714.319| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.16 r_work: 0.3494 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3363 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6564 Z= 0.183 Angle : 0.545 5.478 8921 Z= 0.285 Chirality : 0.043 0.410 1042 Planarity : 0.004 0.054 1133 Dihedral : 3.956 20.014 890 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.19 % Allowed : 17.23 % Favored : 80.58 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.27), residues: 836 helix: 1.68 (0.22), residues: 470 sheet: -1.57 (0.51), residues: 76 loop : -0.18 (0.34), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 141 HIS 0.006 0.001 HIS B 701 PHE 0.027 0.002 PHE B 126 TYR 0.011 0.001 TYR B 694 ARG 0.005 0.001 ARG B 324 Details of bonding type rmsd hydrogen bonds : bond 0.04292 ( 408) hydrogen bonds : angle 4.65902 ( 1179) covalent geometry : bond 0.00413 ( 6564) covalent geometry : angle 0.54461 ( 8921) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 235 LEU cc_start: 0.6157 (pp) cc_final: 0.5504 (mt) REVERT: B 253 ARG cc_start: 0.6901 (mtp85) cc_final: 0.6658 (mtp85) REVERT: B 389 SER cc_start: 0.8475 (t) cc_final: 0.8256 (m) REVERT: B 714 ASP cc_start: 0.8596 (t0) cc_final: 0.8281 (t0) outliers start: 15 outliers final: 10 residues processed: 120 average time/residue: 0.3652 time to fit residues: 61.5094 Evaluate side-chains 100 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 577 ASN Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 701 HIS Chi-restraints excluded: chain B residue 716 SER Chi-restraints excluded: chain B residue 846 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 5 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 79 optimal weight: 0.0770 chunk 55 optimal weight: 0.4980 chunk 9 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 68 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 277 ASN ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.175329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.141740 restraints weight = 23275.921| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.14 r_work: 0.3486 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3360 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6564 Z= 0.147 Angle : 0.511 5.247 8921 Z= 0.265 Chirality : 0.043 0.409 1042 Planarity : 0.004 0.050 1133 Dihedral : 3.818 19.802 890 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.04 % Allowed : 18.10 % Favored : 79.85 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.28), residues: 836 helix: 1.85 (0.22), residues: 471 sheet: -1.55 (0.51), residues: 76 loop : -0.15 (0.35), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 750 HIS 0.005 0.001 HIS B 701 PHE 0.013 0.001 PHE B 126 TYR 0.010 0.001 TYR B 694 ARG 0.002 0.000 ARG B 253 Details of bonding type rmsd hydrogen bonds : bond 0.03931 ( 408) hydrogen bonds : angle 4.50532 ( 1179) covalent geometry : bond 0.00327 ( 6564) covalent geometry : angle 0.51058 ( 8921) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 235 LEU cc_start: 0.6524 (pp) cc_final: 0.5876 (mp) REVERT: B 253 ARG cc_start: 0.6992 (mtp85) cc_final: 0.6587 (mtp85) REVERT: B 519 ARG cc_start: 0.7568 (mmm-85) cc_final: 0.7297 (mmm-85) REVERT: B 714 ASP cc_start: 0.8520 (t0) cc_final: 0.8195 (t0) outliers start: 14 outliers final: 11 residues processed: 109 average time/residue: 0.3387 time to fit residues: 51.8669 Evaluate side-chains 102 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 545 SER Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 701 HIS Chi-restraints excluded: chain B residue 716 SER Chi-restraints excluded: chain B residue 846 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 30 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 74 optimal weight: 0.1980 chunk 23 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 577 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.173217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.139070 restraints weight = 23449.192| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.11 r_work: 0.3449 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6564 Z= 0.163 Angle : 0.520 5.683 8921 Z= 0.269 Chirality : 0.043 0.410 1042 Planarity : 0.004 0.049 1133 Dihedral : 3.793 19.415 890 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.48 % Allowed : 17.66 % Favored : 79.85 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.28), residues: 836 helix: 1.94 (0.23), residues: 468 sheet: -1.58 (0.52), residues: 76 loop : -0.17 (0.35), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 750 HIS 0.005 0.001 HIS B 523 PHE 0.013 0.001 PHE B 126 TYR 0.011 0.001 TYR B 694 ARG 0.003 0.000 ARG B 253 Details of bonding type rmsd hydrogen bonds : bond 0.03878 ( 408) hydrogen bonds : angle 4.41516 ( 1179) covalent geometry : bond 0.00365 ( 6564) covalent geometry : angle 0.52034 ( 8921) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 235 LEU cc_start: 0.6726 (pp) cc_final: 0.6271 (mp) REVERT: B 253 ARG cc_start: 0.7128 (mtp85) cc_final: 0.6762 (mtp85) REVERT: B 405 MET cc_start: 0.7293 (mmt) cc_final: 0.6440 (mmt) REVERT: B 470 ILE cc_start: 0.7224 (mt) cc_final: 0.6892 (mt) REVERT: B 492 GLU cc_start: 0.7000 (tt0) cc_final: 0.6677 (tp30) REVERT: B 519 ARG cc_start: 0.7580 (mmm-85) cc_final: 0.7318 (mmm-85) outliers start: 17 outliers final: 13 residues processed: 107 average time/residue: 0.3188 time to fit residues: 48.3230 Evaluate side-chains 101 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 545 SER Chi-restraints excluded: chain B residue 577 ASN Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 716 SER Chi-restraints excluded: chain B residue 846 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 10 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 25 optimal weight: 0.4980 chunk 39 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 577 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.171197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.137478 restraints weight = 23622.919| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 2.03 r_work: 0.3424 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.3803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6564 Z= 0.190 Angle : 0.530 5.460 8921 Z= 0.276 Chirality : 0.043 0.412 1042 Planarity : 0.004 0.047 1133 Dihedral : 3.817 18.074 890 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.77 % Allowed : 19.12 % Favored : 78.10 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.28), residues: 836 helix: 1.89 (0.23), residues: 468 sheet: -1.59 (0.52), residues: 76 loop : -0.19 (0.35), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 750 HIS 0.005 0.001 HIS B 391 PHE 0.011 0.001 PHE B 126 TYR 0.011 0.001 TYR B 694 ARG 0.002 0.000 ARG B 857 Details of bonding type rmsd hydrogen bonds : bond 0.03983 ( 408) hydrogen bonds : angle 4.41924 ( 1179) covalent geometry : bond 0.00433 ( 6564) covalent geometry : angle 0.53017 ( 8921) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 235 LEU cc_start: 0.7021 (pp) cc_final: 0.6546 (mt) REVERT: B 253 ARG cc_start: 0.7140 (mtp85) cc_final: 0.6782 (mtp85) REVERT: B 405 MET cc_start: 0.7420 (mmt) cc_final: 0.6458 (mmt) REVERT: B 470 ILE cc_start: 0.7366 (mt) cc_final: 0.7106 (mt) REVERT: B 492 GLU cc_start: 0.7112 (tt0) cc_final: 0.6860 (tp30) REVERT: B 519 ARG cc_start: 0.7367 (mmm-85) cc_final: 0.7143 (mmm-85) outliers start: 19 outliers final: 15 residues processed: 105 average time/residue: 0.3475 time to fit residues: 51.0244 Evaluate side-chains 104 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 545 SER Chi-restraints excluded: chain B residue 655 THR Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 701 HIS Chi-restraints excluded: chain B residue 716 SER Chi-restraints excluded: chain B residue 846 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 12 optimal weight: 0.5980 chunk 80 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 76 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 577 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.171195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.137391 restraints weight = 23274.156| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 2.09 r_work: 0.3425 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.4056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6564 Z= 0.160 Angle : 0.515 5.368 8921 Z= 0.266 Chirality : 0.043 0.420 1042 Planarity : 0.004 0.049 1133 Dihedral : 3.744 17.499 890 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.19 % Allowed : 20.00 % Favored : 77.81 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.28), residues: 836 helix: 1.99 (0.23), residues: 469 sheet: -1.46 (0.54), residues: 76 loop : -0.20 (0.35), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 750 HIS 0.005 0.001 HIS B 391 PHE 0.011 0.001 PHE B 126 TYR 0.010 0.001 TYR B 694 ARG 0.002 0.000 ARG B 253 Details of bonding type rmsd hydrogen bonds : bond 0.03858 ( 408) hydrogen bonds : angle 4.35230 ( 1179) covalent geometry : bond 0.00358 ( 6564) covalent geometry : angle 0.51457 ( 8921) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 162 GLU cc_start: 0.7838 (tm-30) cc_final: 0.7550 (tm-30) REVERT: B 235 LEU cc_start: 0.7283 (pp) cc_final: 0.6837 (mt) REVERT: B 253 ARG cc_start: 0.7188 (mtp85) cc_final: 0.6857 (mtp85) REVERT: B 405 MET cc_start: 0.7356 (mmt) cc_final: 0.6412 (mmt) REVERT: B 835 ILE cc_start: 0.8692 (tp) cc_final: 0.8203 (mt) outliers start: 15 outliers final: 12 residues processed: 106 average time/residue: 0.3273 time to fit residues: 49.2843 Evaluate side-chains 106 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 560 ASP Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 701 HIS Chi-restraints excluded: chain B residue 716 SER Chi-restraints excluded: chain B residue 846 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 0 optimal weight: 5.9990 chunk 23 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 67 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 577 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.168515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.134744 restraints weight = 23379.511| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.05 r_work: 0.3394 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.4412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6564 Z= 0.194 Angle : 0.541 5.845 8921 Z= 0.283 Chirality : 0.044 0.417 1042 Planarity : 0.004 0.051 1133 Dihedral : 3.871 17.236 890 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.04 % Allowed : 20.88 % Favored : 77.08 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.28), residues: 836 helix: 1.82 (0.22), residues: 468 sheet: -1.41 (0.55), residues: 76 loop : -0.31 (0.35), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 750 HIS 0.006 0.001 HIS B 391 PHE 0.013 0.001 PHE B 685 TYR 0.010 0.001 TYR B 691 ARG 0.003 0.000 ARG B 253 Details of bonding type rmsd hydrogen bonds : bond 0.04069 ( 408) hydrogen bonds : angle 4.41684 ( 1179) covalent geometry : bond 0.00441 ( 6564) covalent geometry : angle 0.54131 ( 8921) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 226 ASP cc_start: 0.7833 (t0) cc_final: 0.7619 (t70) REVERT: B 235 LEU cc_start: 0.7324 (pp) cc_final: 0.7109 (mp) REVERT: B 253 ARG cc_start: 0.7250 (mtp85) cc_final: 0.7033 (mtp85) REVERT: B 405 MET cc_start: 0.7438 (mmt) cc_final: 0.6470 (mmt) REVERT: B 423 ASP cc_start: 0.8576 (m-30) cc_final: 0.8252 (m-30) REVERT: B 440 LEU cc_start: 0.9066 (tp) cc_final: 0.8849 (tp) REVERT: B 835 ILE cc_start: 0.8722 (tp) cc_final: 0.8234 (mt) outliers start: 14 outliers final: 13 residues processed: 101 average time/residue: 0.3457 time to fit residues: 49.3775 Evaluate side-chains 100 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 560 ASP Chi-restraints excluded: chain B residue 655 THR Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 701 HIS Chi-restraints excluded: chain B residue 716 SER Chi-restraints excluded: chain B residue 846 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 66 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 82 optimal weight: 9.9990 chunk 54 optimal weight: 0.4980 chunk 14 optimal weight: 0.4980 chunk 17 optimal weight: 0.5980 chunk 55 optimal weight: 0.3980 chunk 51 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.170550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.137029 restraints weight = 23291.839| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 2.07 r_work: 0.3419 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.4494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6564 Z= 0.139 Angle : 0.506 5.392 8921 Z= 0.262 Chirality : 0.042 0.412 1042 Planarity : 0.004 0.050 1133 Dihedral : 3.717 16.446 890 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.75 % Allowed : 21.02 % Favored : 77.23 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.28), residues: 836 helix: 2.08 (0.22), residues: 467 sheet: -1.33 (0.55), residues: 76 loop : -0.28 (0.34), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 750 HIS 0.005 0.001 HIS B 701 PHE 0.009 0.001 PHE B 126 TYR 0.009 0.001 TYR B 694 ARG 0.002 0.000 ARG B 253 Details of bonding type rmsd hydrogen bonds : bond 0.03797 ( 408) hydrogen bonds : angle 4.33272 ( 1179) covalent geometry : bond 0.00312 ( 6564) covalent geometry : angle 0.50612 ( 8921) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 253 ARG cc_start: 0.7256 (mtp85) cc_final: 0.6976 (mtp85) REVERT: B 405 MET cc_start: 0.7440 (mmt) cc_final: 0.6538 (mmt) REVERT: B 423 ASP cc_start: 0.8491 (m-30) cc_final: 0.8148 (m-30) REVERT: B 440 LEU cc_start: 0.9032 (tp) cc_final: 0.8808 (tp) REVERT: B 835 ILE cc_start: 0.8703 (tp) cc_final: 0.8202 (mt) outliers start: 12 outliers final: 10 residues processed: 101 average time/residue: 0.4034 time to fit residues: 57.9914 Evaluate side-chains 102 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 1.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 556 MET Chi-restraints excluded: chain B residue 655 THR Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 716 SER Chi-restraints excluded: chain B residue 846 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 64 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 78 optimal weight: 0.0970 chunk 5 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.169438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.132714 restraints weight = 23250.027| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 1.99 r_work: 0.3410 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.4601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6564 Z= 0.161 Angle : 0.521 5.710 8921 Z= 0.271 Chirality : 0.043 0.414 1042 Planarity : 0.004 0.050 1133 Dihedral : 3.724 15.723 890 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.90 % Allowed : 20.88 % Favored : 77.23 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.28), residues: 836 helix: 2.04 (0.22), residues: 467 sheet: -1.44 (0.54), residues: 76 loop : -0.32 (0.34), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 750 HIS 0.005 0.001 HIS B 701 PHE 0.010 0.001 PHE B 685 TYR 0.010 0.001 TYR B 694 ARG 0.002 0.000 ARG B 253 Details of bonding type rmsd hydrogen bonds : bond 0.03859 ( 408) hydrogen bonds : angle 4.34154 ( 1179) covalent geometry : bond 0.00366 ( 6564) covalent geometry : angle 0.52135 ( 8921) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 253 ARG cc_start: 0.7262 (mtp85) cc_final: 0.7050 (mtp85) REVERT: B 405 MET cc_start: 0.7380 (mmt) cc_final: 0.6509 (mmt) REVERT: B 423 ASP cc_start: 0.8498 (m-30) cc_final: 0.8150 (m-30) REVERT: B 440 LEU cc_start: 0.9018 (tp) cc_final: 0.8764 (tp) REVERT: B 835 ILE cc_start: 0.8673 (tp) cc_final: 0.8169 (mt) outliers start: 13 outliers final: 12 residues processed: 101 average time/residue: 0.3498 time to fit residues: 50.4852 Evaluate side-chains 103 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 556 MET Chi-restraints excluded: chain B residue 655 THR Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 701 HIS Chi-restraints excluded: chain B residue 716 SER Chi-restraints excluded: chain B residue 846 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 5 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 50 optimal weight: 0.5980 chunk 31 optimal weight: 0.4980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.168858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.131998 restraints weight = 23325.738| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.00 r_work: 0.3401 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.4795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6564 Z= 0.170 Angle : 0.525 5.766 8921 Z= 0.274 Chirality : 0.043 0.414 1042 Planarity : 0.004 0.049 1133 Dihedral : 3.746 16.334 890 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.04 % Allowed : 20.58 % Favored : 77.37 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.28), residues: 836 helix: 2.04 (0.22), residues: 467 sheet: -1.43 (0.53), residues: 76 loop : -0.35 (0.35), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 750 HIS 0.005 0.001 HIS B 701 PHE 0.011 0.001 PHE B 685 TYR 0.009 0.001 TYR B 694 ARG 0.002 0.000 ARG B 511 Details of bonding type rmsd hydrogen bonds : bond 0.03900 ( 408) hydrogen bonds : angle 4.37534 ( 1179) covalent geometry : bond 0.00387 ( 6564) covalent geometry : angle 0.52519 ( 8921) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8548.78 seconds wall clock time: 148 minutes 26.50 seconds (8906.50 seconds total)