Starting phenix.real_space_refine on Sat Apr 26 20:09:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rr0_24649/04_2025/7rr0_24649.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rr0_24649/04_2025/7rr0_24649.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rr0_24649/04_2025/7rr0_24649.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rr0_24649/04_2025/7rr0_24649.map" model { file = "/net/cci-nas-00/data/ceres_data/7rr0_24649/04_2025/7rr0_24649.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rr0_24649/04_2025/7rr0_24649.cif" } resolution = 3.12 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= 0.002 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 18 5.16 5 C 2088 2.51 5 N 561 2.21 5 O 630 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 3297 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1528 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 182} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 937 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "C" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.63, per 1000 atoms: 0.80 Number of scatterers: 3297 At special positions: 0 Unit cell: (58.3, 68.9, 104.94, 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 18 16.00 O 630 8.00 N 561 7.00 C 2088 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.02 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 101 " - pdb=" SG CYS B 106 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 89 " distance=2.04 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: 0.75 Conformation dependent library (CDL) restraints added in 427.4 milliseconds 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 774 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 8 sheets defined 10.9% alpha, 31.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.773A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.329A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'B' and resid 87 through 91 removed outlier: 3.640A pdb=" N THR B 91 " --> pdb=" O SER B 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 84 removed outlier: 4.060A pdb=" N PHE C 84 " --> pdb=" O PRO C 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.868A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS A 356 " --> pdb=" O ALA A 397 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 391 through 392 removed outlier: 3.519A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'B' and resid 3 through 6 removed outlier: 3.528A pdb=" N SER B 25 " --> pdb=" O GLN B 3 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 11 removed outlier: 7.033A pdb=" N GLU B 10 " --> pdb=" O THR B 120 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL B 34 " --> pdb=" O TRP B 50 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N TRP B 50 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N TRP B 36 " --> pdb=" O ILE B 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 11 removed outlier: 7.033A pdb=" N GLU B 10 " --> pdb=" O THR B 120 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 4 through 7 removed outlier: 3.750A pdb=" N SER C 7 " --> pdb=" O SER C 22 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER C 22 " --> pdb=" O SER C 7 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA C 19 " --> pdb=" O ILE C 76 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE C 76 " --> pdb=" O ALA C 19 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.528A pdb=" N THR C 103 " --> pdb=" O TYR C 87 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N LEU C 34 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N TYR C 50 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) 102 hydrogen bonds defined for protein. 252 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: 0.83 Time building geometry restraints manager: 0.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1053 1.34 - 1.46: 887 1.46 - 1.59: 1418 1.59 - 1.71: 0 1.71 - 1.83: 22 Bond restraints: 3380 Sorted by residual: bond pdb=" C1 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.41e+00 bond pdb=" CB PRO A 479 " pdb=" CG PRO A 479 " ideal model delta sigma weight residual 1.492 1.572 -0.080 5.00e-02 4.00e+02 2.53e+00 bond pdb=" CG LEU C 48 " pdb=" CD1 LEU C 48 " ideal model delta sigma weight residual 1.521 1.473 0.048 3.30e-02 9.18e+02 2.10e+00 bond pdb=" CB GLN B 6 " pdb=" CG GLN B 6 " ideal model delta sigma weight residual 1.520 1.479 0.041 3.00e-02 1.11e+03 1.87e+00 bond pdb=" CA THR A 470 " pdb=" C THR A 470 " ideal model delta sigma weight residual 1.525 1.542 -0.017 1.35e-02 5.49e+03 1.63e+00 ... (remaining 3375 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 4402 2.24 - 4.48: 167 4.48 - 6.73: 18 6.73 - 8.97: 6 8.97 - 11.21: 2 Bond angle restraints: 4595 Sorted by residual: angle pdb=" C GLY C 51 " pdb=" N ALA C 52 " pdb=" CA ALA C 52 " ideal model delta sigma weight residual 121.54 129.41 -7.87 1.91e+00 2.74e-01 1.70e+01 angle pdb=" OG1 THR A 470 " pdb=" CB THR A 470 " pdb=" CG2 THR A 470 " ideal model delta sigma weight residual 109.30 101.40 7.90 2.00e+00 2.50e-01 1.56e+01 angle pdb=" CA PRO A 479 " pdb=" N PRO A 479 " pdb=" CD PRO A 479 " ideal model delta sigma weight residual 112.00 107.13 4.87 1.40e+00 5.10e-01 1.21e+01 angle pdb=" C ARG A 403 " pdb=" N GLY A 404 " pdb=" CA GLY A 404 " ideal model delta sigma weight residual 119.99 123.77 -3.78 1.13e+00 7.83e-01 1.12e+01 angle pdb=" CA ARG A 403 " pdb=" CB ARG A 403 " pdb=" CG ARG A 403 " ideal model delta sigma weight residual 114.10 120.54 -6.44 2.00e+00 2.50e-01 1.04e+01 ... (remaining 4590 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.43: 1807 14.43 - 28.86: 157 28.86 - 43.28: 37 43.28 - 57.71: 12 57.71 - 72.14: 3 Dihedral angle restraints: 2016 sinusoidal: 797 harmonic: 1219 Sorted by residual: dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 96 " pdb=" CB CYS B 96 " ideal model delta sinusoidal sigma weight residual -86.00 -112.35 26.35 1 1.00e+01 1.00e-02 9.97e+00 dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual 93.00 118.76 -25.76 1 1.00e+01 1.00e-02 9.54e+00 dihedral pdb=" CA LEU A 461 " pdb=" C LEU A 461 " pdb=" N LYS A 462 " pdb=" CA LYS A 462 " ideal model delta harmonic sigma weight residual 180.00 164.57 15.43 0 5.00e+00 4.00e-02 9.52e+00 ... (remaining 2013 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 290 0.040 - 0.080: 125 0.080 - 0.119: 57 0.119 - 0.159: 16 0.159 - 0.199: 6 Chirality restraints: 494 Sorted by residual: chirality pdb=" CB THR A 470 " pdb=" CA THR A 470 " pdb=" OG1 THR A 470 " pdb=" CG2 THR A 470 " both_signs ideal model delta sigma weight residual False 2.55 2.75 -0.20 2.00e-01 2.50e+01 9.88e-01 chirality pdb=" CB THR B 91 " pdb=" CA THR B 91 " pdb=" OG1 THR B 91 " pdb=" CG2 THR B 91 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 8.73e-01 chirality pdb=" CA VAL B 52 " pdb=" N VAL B 52 " pdb=" C VAL B 52 " pdb=" CB VAL B 52 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.18 2.00e-01 2.50e+01 8.51e-01 ... (remaining 491 not shown) Planarity restraints: 596 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 68 " 0.011 2.00e-02 2.50e+03 2.15e-02 4.64e+00 pdb=" C VAL B 68 " -0.037 2.00e-02 2.50e+03 pdb=" O VAL B 68 " 0.014 2.00e-02 2.50e+03 pdb=" N THR B 69 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 520 " -0.036 5.00e-02 4.00e+02 5.38e-02 4.63e+00 pdb=" N PRO A 521 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 521 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 521 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 91 " 0.010 2.00e-02 2.50e+03 2.04e-02 4.15e+00 pdb=" C GLN C 91 " -0.035 2.00e-02 2.50e+03 pdb=" O GLN C 91 " 0.013 2.00e-02 2.50e+03 pdb=" N TYR C 92 " 0.012 2.00e-02 2.50e+03 ... (remaining 593 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 1035 2.84 - 3.36: 2598 3.36 - 3.87: 5389 3.87 - 4.39: 5842 4.39 - 4.90: 10738 Nonbonded interactions: 25602 Sorted by model distance: nonbonded pdb=" OD2 ASP B 73 " pdb=" OG1 THR B 76 " model vdw 2.327 3.040 nonbonded pdb=" OD1 ASP A 442 " pdb=" OH TYR A 451 " model vdw 2.332 3.040 nonbonded pdb=" O ASN A 439 " pdb=" OG SER A 443 " model vdw 2.340 3.040 nonbonded pdb=" O VAL A 367 " pdb=" OG SER A 371 " model vdw 2.343 3.040 nonbonded pdb=" OE2 GLU B 46 " pdb=" NH1 ARG B 63 " model vdw 2.352 3.120 ... (remaining 25597 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: 0.240 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.000 Find NCS groups from input model: 0.030 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 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 0.080 3387 Z= 0.211 Angle : 0.970 11.211 4609 Z= 0.521 Chirality : 0.056 0.199 494 Planarity : 0.008 0.065 596 Dihedral : 12.282 72.140 1221 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.12 (0.38), residues: 416 helix: -1.69 (0.96), residues: 25 sheet: 0.90 (0.44), residues: 131 loop : -0.12 (0.35), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP B 50 PHE 0.011 0.001 PHE A 374 TYR 0.011 0.001 TYR B 95 ARG 0.014 0.001 ARG C 78 Details of bonding type rmsd hydrogen bonds : bond 0.24991 ( 98) hydrogen bonds : angle 10.24079 ( 252) SS BOND : bond 0.00479 ( 7) SS BOND : angle 1.49150 ( 14) covalent geometry : bond 0.00449 ( 3380) covalent geometry : angle 0.96770 ( 4595) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 64 PHE cc_start: 0.4991 (m-10) cc_final: 0.4646 (m-10) REVERT: B 73 ASP cc_start: 0.7696 (t70) cc_final: 0.7373 (t70) REVERT: C 37 TYR cc_start: 0.8370 (m-80) cc_final: 0.8165 (m-80) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.2064 time to fit residues: 27.8113 Evaluate side-chains 88 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 3.9990 chunk 31 optimal weight: 0.0770 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 20.0000 chunk 12 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 9.9990 overall best weight: 1.7744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 ASN A 360 ASN B 6 GLN B 59 ASN C 38 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.134940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.107402 restraints weight = 5255.238| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 3.08 r_work: 0.3359 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.116 3387 Z= 0.254 Angle : 0.730 14.663 4609 Z= 0.385 Chirality : 0.049 0.276 494 Planarity : 0.005 0.032 596 Dihedral : 5.850 57.944 490 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 4.21 % Allowed : 11.80 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.15 (0.39), residues: 416 helix: -1.89 (0.95), residues: 26 sheet: 0.83 (0.41), residues: 151 loop : -0.08 (0.37), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 50 PHE 0.019 0.002 PHE A 377 TYR 0.017 0.002 TYR B 95 ARG 0.007 0.001 ARG A 509 Details of bonding type rmsd hydrogen bonds : bond 0.04425 ( 98) hydrogen bonds : angle 6.79032 ( 252) SS BOND : bond 0.01179 ( 7) SS BOND : angle 2.60697 ( 14) covalent geometry : bond 0.00616 ( 3380) covalent geometry : angle 0.71703 ( 4595) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 471 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.6129 (mp0) REVERT: B 12 LYS cc_start: 0.9119 (OUTLIER) cc_final: 0.8911 (mtpt) REVERT: B 43 GLN cc_start: 0.8897 (mp10) cc_final: 0.8672 (mp10) REVERT: B 73 ASP cc_start: 0.8230 (t70) cc_final: 0.7709 (t70) REVERT: C 24 ARG cc_start: 0.7212 (mmm-85) cc_final: 0.6848 (mmm-85) outliers start: 15 outliers final: 8 residues processed: 96 average time/residue: 0.2137 time to fit residues: 23.7986 Evaluate side-chains 89 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 12 LYS Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain C residue 29 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 40 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 35 optimal weight: 0.4980 chunk 30 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 1 GLN ** B 6 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 = 0.3859 r_free = 0.3859 target = 0.136340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.109487 restraints weight = 5076.953| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.99 r_work: 0.3395 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 3387 Z= 0.146 Angle : 0.626 12.101 4609 Z= 0.321 Chirality : 0.044 0.139 494 Planarity : 0.004 0.029 596 Dihedral : 5.435 53.847 490 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.93 % Allowed : 14.61 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.06 (0.39), residues: 416 helix: -2.28 (0.82), residues: 32 sheet: 0.74 (0.40), residues: 159 loop : -0.03 (0.38), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 PHE 0.012 0.001 PHE A 377 TYR 0.014 0.001 TYR B 95 ARG 0.005 0.000 ARG C 55 Details of bonding type rmsd hydrogen bonds : bond 0.03571 ( 98) hydrogen bonds : angle 6.34887 ( 252) SS BOND : bond 0.00786 ( 7) SS BOND : angle 2.01487 ( 14) covalent geometry : bond 0.00355 ( 3380) covalent geometry : angle 0.61703 ( 4595) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 471 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6127 (mp0) REVERT: B 12 LYS cc_start: 0.8956 (OUTLIER) cc_final: 0.8720 (mtpt) REVERT: B 43 GLN cc_start: 0.8835 (mp10) cc_final: 0.8531 (mp10) REVERT: B 73 ASP cc_start: 0.8198 (t70) cc_final: 0.7535 (t70) outliers start: 14 outliers final: 8 residues processed: 97 average time/residue: 0.2048 time to fit residues: 23.0873 Evaluate side-chains 93 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 12 LYS Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 29 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 11 optimal weight: 0.0970 chunk 26 optimal weight: 0.9980 chunk 15 optimal weight: 0.0470 chunk 39 optimal weight: 0.6980 chunk 20 optimal weight: 0.0000 chunk 31 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.3680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 1 GLN B 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.139203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.112209 restraints weight = 5193.867| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 3.10 r_work: 0.3432 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 3387 Z= 0.113 Angle : 0.611 14.729 4609 Z= 0.312 Chirality : 0.043 0.176 494 Planarity : 0.004 0.032 596 Dihedral : 5.170 53.103 490 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.53 % Allowed : 18.54 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.06 (0.39), residues: 416 helix: -2.19 (0.87), residues: 32 sheet: 0.83 (0.42), residues: 147 loop : -0.07 (0.36), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 47 PHE 0.011 0.001 PHE A 377 TYR 0.009 0.001 TYR A 451 ARG 0.006 0.001 ARG B 87 Details of bonding type rmsd hydrogen bonds : bond 0.03233 ( 98) hydrogen bonds : angle 5.93799 ( 252) SS BOND : bond 0.00736 ( 7) SS BOND : angle 1.88420 ( 14) covalent geometry : bond 0.00277 ( 3380) covalent geometry : angle 0.60263 ( 4595) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 12 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8609 (mtpt) REVERT: B 43 GLN cc_start: 0.8829 (mp10) cc_final: 0.8039 (mp10) REVERT: B 66 GLU cc_start: 0.7948 (pm20) cc_final: 0.7604 (tm-30) REVERT: B 73 ASP cc_start: 0.8172 (t70) cc_final: 0.7603 (t70) REVERT: C 46 ARG cc_start: 0.8519 (ttp-170) cc_final: 0.8253 (ttp-170) outliers start: 9 outliers final: 7 residues processed: 92 average time/residue: 0.2245 time to fit residues: 23.8432 Evaluate side-chains 85 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 12 LYS Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain C residue 12 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 23 optimal weight: 0.2980 chunk 34 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN B 59 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.135793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.108489 restraints weight = 5243.107| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 3.10 r_work: 0.3371 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 3387 Z= 0.157 Angle : 0.638 15.555 4609 Z= 0.327 Chirality : 0.044 0.217 494 Planarity : 0.004 0.030 596 Dihedral : 5.349 54.768 490 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.53 % Allowed : 19.66 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.11 (0.39), residues: 416 helix: -2.01 (0.93), residues: 32 sheet: 0.74 (0.40), residues: 162 loop : -0.02 (0.37), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 PHE 0.011 0.001 PHE A 377 TYR 0.014 0.001 TYR B 95 ARG 0.005 0.000 ARG B 87 Details of bonding type rmsd hydrogen bonds : bond 0.03274 ( 98) hydrogen bonds : angle 5.93217 ( 252) SS BOND : bond 0.00862 ( 7) SS BOND : angle 1.90749 ( 14) covalent geometry : bond 0.00381 ( 3380) covalent geometry : angle 0.63039 ( 4595) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 12 LYS cc_start: 0.8958 (OUTLIER) cc_final: 0.8652 (mtpt) REVERT: B 43 GLN cc_start: 0.8725 (mp10) cc_final: 0.7902 (mp10) REVERT: B 66 GLU cc_start: 0.8015 (pm20) cc_final: 0.7598 (tm-30) REVERT: B 73 ASP cc_start: 0.8152 (t70) cc_final: 0.7501 (t70) REVERT: B 107 TYR cc_start: 0.7911 (t80) cc_final: 0.7604 (t80) REVERT: C 46 ARG cc_start: 0.8562 (ttp-170) cc_final: 0.8290 (ttp-170) outliers start: 9 outliers final: 7 residues processed: 89 average time/residue: 0.2334 time to fit residues: 23.8880 Evaluate side-chains 87 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain B residue 12 LYS Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 29 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 39 optimal weight: 0.7980 chunk 32 optimal weight: 8.9990 chunk 34 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 14 optimal weight: 0.0020 overall best weight: 0.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.134411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.107437 restraints weight = 5337.788| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 3.10 r_work: 0.3352 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.4078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 3387 Z= 0.153 Angle : 0.635 15.366 4609 Z= 0.326 Chirality : 0.044 0.202 494 Planarity : 0.004 0.031 596 Dihedral : 5.336 54.279 490 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 4.21 % Allowed : 18.82 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.08 (0.39), residues: 416 helix: -1.99 (0.94), residues: 32 sheet: 0.75 (0.41), residues: 158 loop : -0.05 (0.37), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 PHE 0.011 0.001 PHE A 377 TYR 0.013 0.001 TYR B 95 ARG 0.007 0.001 ARG B 87 Details of bonding type rmsd hydrogen bonds : bond 0.03273 ( 98) hydrogen bonds : angle 5.83527 ( 252) SS BOND : bond 0.00929 ( 7) SS BOND : angle 1.91406 ( 14) covalent geometry : bond 0.00373 ( 3380) covalent geometry : angle 0.62743 ( 4595) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 471 GLU cc_start: 0.7096 (OUTLIER) cc_final: 0.6180 (mp0) REVERT: B 43 GLN cc_start: 0.8786 (mp10) cc_final: 0.7996 (mp10) REVERT: B 66 GLU cc_start: 0.7996 (pm20) cc_final: 0.7640 (tm-30) REVERT: B 73 ASP cc_start: 0.8073 (t70) cc_final: 0.7401 (t70) REVERT: B 107 TYR cc_start: 0.7963 (t80) cc_final: 0.7595 (t80) REVERT: C 5 THR cc_start: 0.7586 (m) cc_final: 0.7193 (p) outliers start: 15 outliers final: 10 residues processed: 96 average time/residue: 0.2232 time to fit residues: 24.6679 Evaluate side-chains 92 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 29 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 0.5980 chunk 21 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 4 optimal weight: 0.0980 chunk 12 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 32 optimal weight: 8.9990 chunk 19 optimal weight: 0.4980 chunk 28 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN B 59 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.137092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.110109 restraints weight = 5172.174| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 3.09 r_work: 0.3395 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.4092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 3387 Z= 0.122 Angle : 0.651 14.956 4609 Z= 0.328 Chirality : 0.044 0.188 494 Planarity : 0.004 0.029 596 Dihedral : 5.216 53.407 490 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.25 % Allowed : 21.07 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.15 (0.39), residues: 416 helix: -2.03 (0.92), residues: 32 sheet: 0.84 (0.41), residues: 151 loop : -0.00 (0.37), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 47 PHE 0.010 0.001 PHE A 377 TYR 0.010 0.001 TYR A 380 ARG 0.006 0.001 ARG C 55 Details of bonding type rmsd hydrogen bonds : bond 0.03158 ( 98) hydrogen bonds : angle 5.78624 ( 252) SS BOND : bond 0.00893 ( 7) SS BOND : angle 1.88657 ( 14) covalent geometry : bond 0.00300 ( 3380) covalent geometry : angle 0.64376 ( 4595) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 444 LYS cc_start: 0.8236 (tppt) cc_final: 0.8011 (tppt) REVERT: B 43 GLN cc_start: 0.8758 (mp10) cc_final: 0.8018 (mp10) REVERT: B 73 ASP cc_start: 0.8109 (t70) cc_final: 0.7451 (t70) REVERT: B 107 TYR cc_start: 0.7921 (t80) cc_final: 0.7503 (t80) REVERT: C 5 THR cc_start: 0.7499 (m) cc_final: 0.7092 (p) outliers start: 8 outliers final: 8 residues processed: 92 average time/residue: 0.2079 time to fit residues: 22.1664 Evaluate side-chains 90 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain C residue 29 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 0 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 13 optimal weight: 0.3980 chunk 28 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.134891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.107672 restraints weight = 5183.975| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 3.08 r_work: 0.3363 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.4225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 3387 Z= 0.157 Angle : 0.667 14.928 4609 Z= 0.340 Chirality : 0.044 0.189 494 Planarity : 0.004 0.029 596 Dihedral : 5.358 54.627 490 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.81 % Allowed : 21.35 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.15 (0.40), residues: 416 helix: -1.98 (0.93), residues: 32 sheet: 0.66 (0.40), residues: 162 loop : 0.11 (0.39), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 47 PHE 0.010 0.001 PHE A 377 TYR 0.011 0.001 TYR B 95 ARG 0.008 0.001 ARG B 87 Details of bonding type rmsd hydrogen bonds : bond 0.03261 ( 98) hydrogen bonds : angle 5.91385 ( 252) SS BOND : bond 0.00936 ( 7) SS BOND : angle 1.91810 ( 14) covalent geometry : bond 0.00383 ( 3380) covalent geometry : angle 0.65986 ( 4595) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 43 GLN cc_start: 0.8734 (mp10) cc_final: 0.8006 (mp10) REVERT: B 63 ARG cc_start: 0.7807 (ptm-80) cc_final: 0.7483 (ptm160) REVERT: B 66 GLU cc_start: 0.8168 (pm20) cc_final: 0.7717 (tm-30) REVERT: B 73 ASP cc_start: 0.8093 (t70) cc_final: 0.7409 (t70) REVERT: B 107 TYR cc_start: 0.7958 (t80) cc_final: 0.7526 (t80) outliers start: 10 outliers final: 9 residues processed: 94 average time/residue: 0.2187 time to fit residues: 23.6383 Evaluate side-chains 95 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain C residue 29 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 33 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 31 optimal weight: 0.0010 chunk 16 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 35 optimal weight: 0.0980 chunk 25 optimal weight: 0.1980 chunk 30 optimal weight: 0.8980 overall best weight: 0.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN B 59 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.137560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.110336 restraints weight = 5177.628| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 3.10 r_work: 0.3402 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.4214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 3387 Z= 0.120 Angle : 0.649 14.750 4609 Z= 0.329 Chirality : 0.044 0.178 494 Planarity : 0.004 0.032 596 Dihedral : 5.196 53.227 490 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.25 % Allowed : 23.03 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.18 (0.40), residues: 416 helix: -1.97 (0.85), residues: 38 sheet: 0.75 (0.41), residues: 158 loop : 0.16 (0.39), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 47 PHE 0.010 0.001 PHE A 377 TYR 0.014 0.001 TYR A 380 ARG 0.008 0.001 ARG C 55 Details of bonding type rmsd hydrogen bonds : bond 0.03083 ( 98) hydrogen bonds : angle 5.81614 ( 252) SS BOND : bond 0.00884 ( 7) SS BOND : angle 1.89319 ( 14) covalent geometry : bond 0.00296 ( 3380) covalent geometry : angle 0.64183 ( 4595) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 442 ASP cc_start: 0.8206 (t0) cc_final: 0.7364 (t70) REVERT: A 444 LYS cc_start: 0.8262 (tppt) cc_final: 0.7952 (tppt) REVERT: B 43 GLN cc_start: 0.8686 (mp10) cc_final: 0.7974 (mp10) REVERT: B 63 ARG cc_start: 0.7833 (ptm-80) cc_final: 0.7495 (ptm160) REVERT: B 65 GLN cc_start: 0.8335 (tt0) cc_final: 0.7835 (mt0) REVERT: B 66 GLU cc_start: 0.8164 (pm20) cc_final: 0.7719 (tm-30) REVERT: B 73 ASP cc_start: 0.8059 (t70) cc_final: 0.7373 (t70) REVERT: B 107 TYR cc_start: 0.7934 (t80) cc_final: 0.7471 (t80) REVERT: C 24 ARG cc_start: 0.7062 (mmm-85) cc_final: 0.6640 (mmm160) outliers start: 8 outliers final: 8 residues processed: 91 average time/residue: 0.2226 time to fit residues: 23.5037 Evaluate side-chains 91 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain C residue 29 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 31 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.135391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.108222 restraints weight = 5073.390| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 3.05 r_work: 0.3369 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.4336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 3387 Z= 0.155 Angle : 0.683 14.782 4609 Z= 0.348 Chirality : 0.044 0.184 494 Planarity : 0.004 0.029 596 Dihedral : 5.312 54.460 490 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.25 % Allowed : 23.88 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.19 (0.40), residues: 416 helix: -1.95 (0.94), residues: 32 sheet: 0.65 (0.40), residues: 162 loop : 0.17 (0.40), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 47 PHE 0.010 0.001 PHE A 377 TYR 0.014 0.001 TYR A 380 ARG 0.007 0.001 ARG B 87 Details of bonding type rmsd hydrogen bonds : bond 0.03294 ( 98) hydrogen bonds : angle 5.91193 ( 252) SS BOND : bond 0.00929 ( 7) SS BOND : angle 1.92116 ( 14) covalent geometry : bond 0.00378 ( 3380) covalent geometry : angle 0.67560 ( 4595) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 444 LYS cc_start: 0.8271 (tppt) cc_final: 0.7966 (tppt) REVERT: B 43 GLN cc_start: 0.8700 (mp10) cc_final: 0.7999 (mp10) REVERT: B 65 GLN cc_start: 0.8383 (tt0) cc_final: 0.7900 (mt0) REVERT: B 66 GLU cc_start: 0.8140 (pm20) cc_final: 0.7735 (tm-30) REVERT: B 73 ASP cc_start: 0.8100 (t70) cc_final: 0.7396 (t70) REVERT: B 107 TYR cc_start: 0.7967 (t80) cc_final: 0.7521 (t80) REVERT: C 24 ARG cc_start: 0.6950 (mmm-85) cc_final: 0.6647 (mmm160) REVERT: C 80 GLU cc_start: 0.8724 (mm-30) cc_final: 0.8299 (mp0) outliers start: 8 outliers final: 8 residues processed: 88 average time/residue: 0.2185 time to fit residues: 22.3712 Evaluate side-chains 90 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain C residue 29 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.0426 > 50: distance: 22 - 28: 9.178 distance: 28 - 29: 8.617 distance: 29 - 30: 13.579 distance: 29 - 32: 6.075 distance: 30 - 31: 18.393 distance: 30 - 40: 16.732 distance: 32 - 33: 5.903 distance: 33 - 34: 10.753 distance: 33 - 35: 17.567 distance: 34 - 36: 10.173 distance: 35 - 37: 6.332 distance: 36 - 38: 13.420 distance: 37 - 38: 11.221 distance: 38 - 39: 11.336 distance: 40 - 41: 5.469 distance: 41 - 42: 16.265 distance: 41 - 44: 7.244 distance: 42 - 43: 24.075 distance: 42 - 49: 22.624 distance: 44 - 45: 9.482 distance: 45 - 46: 8.110 distance: 46 - 47: 5.501 distance: 49 - 50: 15.797 distance: 50 - 51: 28.553 distance: 50 - 53: 5.448 distance: 51 - 52: 34.610 distance: 51 - 54: 24.868 distance: 54 - 55: 13.822 distance: 55 - 56: 36.125 distance: 56 - 57: 55.298 distance: 56 - 58: 50.702 distance: 58 - 59: 15.132 distance: 59 - 60: 22.848 distance: 59 - 62: 29.232 distance: 60 - 61: 5.311 distance: 60 - 64: 15.400 distance: 62 - 63: 17.779 distance: 64 - 65: 31.507 distance: 65 - 66: 35.204 distance: 65 - 68: 23.902 distance: 66 - 67: 26.827 distance: 66 - 71: 13.567 distance: 68 - 69: 27.489 distance: 68 - 70: 15.939 distance: 71 - 72: 9.282 distance: 71 - 77: 15.278 distance: 72 - 73: 10.453 distance: 72 - 75: 20.984 distance: 73 - 74: 17.884 distance: 73 - 78: 13.231 distance: 75 - 76: 19.757 distance: 76 - 77: 20.544 distance: 78 - 79: 13.847 distance: 79 - 80: 6.075 distance: 79 - 82: 8.761 distance: 80 - 81: 5.961 distance: 82 - 83: 5.463 distance: 83 - 115: 6.142 distance: 84 - 85: 13.482 distance: 85 - 86: 7.697 distance: 85 - 88: 5.673 distance: 86 - 87: 6.055 distance: 86 - 92: 8.979 distance: 88 - 89: 8.578 distance: 89 - 90: 6.543 distance: 89 - 91: 7.549 distance: 92 - 93: 7.789 distance: 93 - 94: 12.234 distance: 94 - 95: 13.134 distance: 94 - 96: 15.891