Starting phenix.real_space_refine on Fri May 9 18:03:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i3s_35155/05_2025/8i3s_35155.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i3s_35155/05_2025/8i3s_35155.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8i3s_35155/05_2025/8i3s_35155.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i3s_35155/05_2025/8i3s_35155.map" model { file = "/net/cci-nas-00/data/ceres_data/8i3s_35155/05_2025/8i3s_35155.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i3s_35155/05_2025/8i3s_35155.cif" } resolution = 3.9 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= -0.003 sd= 0.032 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 16 5.16 5 C 2074 2.51 5 N 554 2.21 5 O 628 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 3272 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1552 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 11, 'TRANS': 184} Chain: "H" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 897 Classifications: {'peptide': 118} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 112} Chain: "L" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 809 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 4, 'TRANS': 101} 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: 3.36, per 1000 atoms: 1.03 Number of scatterers: 3272 At special positions: 0 Unit cell: (67.45, 68.4, 96.9, 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 16 16.00 O 628 8.00 N 554 7.00 C 2074 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=1.56 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=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 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 Links applied NAG-ASN " NAG A1301 " - " ASN A 343 " Time building additional restraints: 0.81 Conformation dependent library (CDL) restraints added in 1.0 seconds 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 768 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 9 sheets defined 10.7% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 337 through 344 removed outlier: 3.873A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 383 through 388 removed outlier: 3.658A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 411 removed outlier: 3.542A pdb=" N GLN A 409 " --> pdb=" O GLU A 406 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'H' and resid 83 through 87 removed outlier: 4.000A pdb=" N THR H 87 " --> pdb=" O SER H 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.725A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG A 509 " --> pdb=" O TRP A 436 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TRP A 436 " --> pdb=" O ARG A 509 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.189A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'H' and resid 6 through 7 removed outlier: 3.679A pdb=" N VAL H 18 " --> pdb=" O LEU H 82 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 12 through 13 removed outlier: 7.060A pdb=" N LYS H 12 " --> pdb=" O SER H 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'H' and resid 56 through 59 removed outlier: 3.670A pdb=" N ARG H 56 " --> pdb=" O ILE H 52 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE H 52 " --> pdb=" O ARG H 56 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N TYR H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ARG H 38 " --> pdb=" O TYR H 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 20 through 24 Processing sheet with id=AA9, first strand: chain 'L' and resid 45 through 46 82 hydrogen bonds defined for protein. 207 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: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 863 1.33 - 1.45: 679 1.45 - 1.57: 1787 1.57 - 1.69: 0 1.69 - 1.82: 20 Bond restraints: 3349 Sorted by residual: bond pdb=" N PRO L 59 " pdb=" CA PRO L 59 " ideal model delta sigma weight residual 1.468 1.440 0.027 7.90e-03 1.60e+04 1.21e+01 bond pdb=" N ASN H 32 " pdb=" CA ASN H 32 " ideal model delta sigma weight residual 1.454 1.492 -0.038 1.19e-02 7.06e+03 1.02e+01 bond pdb=" N PHE L 62 " pdb=" CA PHE L 62 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.21e-02 6.83e+03 6.49e+00 bond pdb=" N ILE L 58 " pdb=" CA ILE L 58 " ideal model delta sigma weight residual 1.461 1.490 -0.029 1.23e-02 6.61e+03 5.41e+00 bond pdb=" CA SER L 63 " pdb=" CB SER L 63 " ideal model delta sigma weight residual 1.529 1.499 0.030 1.54e-02 4.22e+03 3.78e+00 ... (remaining 3344 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.17: 4343 1.17 - 2.34: 152 2.34 - 3.51: 38 3.51 - 4.68: 10 4.68 - 5.85: 4 Bond angle restraints: 4547 Sorted by residual: angle pdb=" CA ALA L 60 " pdb=" C ALA L 60 " pdb=" O ALA L 60 " ideal model delta sigma weight residual 120.81 116.22 4.59 1.15e+00 7.56e-01 1.60e+01 angle pdb=" N PRO L 59 " pdb=" CA PRO L 59 " pdb=" C PRO L 59 " ideal model delta sigma weight residual 113.12 107.27 5.85 1.65e+00 3.67e-01 1.26e+01 angle pdb=" CA PRO L 59 " pdb=" C PRO L 59 " pdb=" O PRO L 59 " ideal model delta sigma weight residual 121.38 118.69 2.69 7.70e-01 1.69e+00 1.22e+01 angle pdb=" C ILE H 31 " pdb=" N ASN H 32 " pdb=" CA ASN H 32 " ideal model delta sigma weight residual 122.87 117.62 5.25 1.61e+00 3.86e-01 1.06e+01 angle pdb=" N PRO L 59 " pdb=" CD PRO L 59 " pdb=" CG PRO L 59 " ideal model delta sigma weight residual 103.20 98.41 4.79 1.50e+00 4.44e-01 1.02e+01 ... (remaining 4542 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.35: 1779 12.35 - 24.70: 150 24.70 - 37.05: 50 37.05 - 49.40: 12 49.40 - 61.75: 9 Dihedral angle restraints: 2000 sinusoidal: 789 harmonic: 1211 Sorted by residual: dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual -86.00 -114.61 28.61 1 1.00e+01 1.00e-02 1.17e+01 dihedral pdb=" CA ARG L 61 " pdb=" CB ARG L 61 " pdb=" CG ARG L 61 " pdb=" CD ARG L 61 " ideal model delta sinusoidal sigma weight residual 180.00 123.29 56.71 3 1.50e+01 4.44e-03 9.41e+00 dihedral pdb=" CA ILE A 434 " pdb=" CB ILE A 434 " pdb=" CG1 ILE A 434 " pdb=" CD1 ILE A 434 " ideal model delta sinusoidal sigma weight residual 60.00 115.51 -55.51 3 1.50e+01 4.44e-03 9.35e+00 ... (remaining 1997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 387 0.046 - 0.092: 74 0.092 - 0.138: 31 0.138 - 0.184: 4 0.184 - 0.230: 1 Chirality restraints: 497 Sorted by residual: chirality pdb=" CA PHE L 62 " pdb=" N PHE L 62 " pdb=" C PHE L 62 " pdb=" CB PHE L 62 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CA ALA L 60 " pdb=" N ALA L 60 " pdb=" C ALA L 60 " pdb=" CB ALA L 60 " both_signs ideal model delta sigma weight residual False 2.48 2.67 -0.18 2.00e-01 2.50e+01 8.11e-01 chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 343 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 7.51e-01 ... (remaining 494 not shown) Planarity restraints: 590 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR L 56 " -0.010 2.00e-02 2.50e+03 1.97e-02 3.88e+00 pdb=" C THR L 56 " 0.034 2.00e-02 2.50e+03 pdb=" O THR L 56 " -0.013 2.00e-02 2.50e+03 pdb=" N GLY L 57 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE H 31 " 0.010 2.00e-02 2.50e+03 1.92e-02 3.69e+00 pdb=" C ILE H 31 " -0.033 2.00e-02 2.50e+03 pdb=" O ILE H 31 " 0.012 2.00e-02 2.50e+03 pdb=" N ASN H 32 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP H 101 " 0.030 5.00e-02 4.00e+02 4.59e-02 3.37e+00 pdb=" N PRO H 102 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO H 102 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO H 102 " 0.023 5.00e-02 4.00e+02 ... (remaining 587 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 560 2.77 - 3.30: 3130 3.30 - 3.83: 5250 3.83 - 4.37: 6115 4.37 - 4.90: 10669 Nonbonded interactions: 25724 Sorted by model distance: nonbonded pdb=" O VAL A 367 " pdb=" OG SER A 371 " model vdw 2.235 3.040 nonbonded pdb=" OG SER A 349 " pdb=" O LEU A 452 " model vdw 2.242 3.040 nonbonded pdb=" NH2 ARG A 457 " pdb=" OD2 ASP A 467 " model vdw 2.301 3.120 nonbonded pdb=" O ASP L 82 " pdb=" OH TYR L 86 " model vdw 2.340 3.040 nonbonded pdb=" OH TYR A 453 " pdb=" OE1 GLN A 493 " model vdw 2.369 3.040 ... (remaining 25719 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 group one per residue 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: 2.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.580 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 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 : 0.009 0.475 3356 Z= 0.457 Angle : 0.984 49.602 4562 Z= 0.514 Chirality : 0.045 0.230 497 Planarity : 0.004 0.046 589 Dihedral : 11.402 61.753 1214 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.54 % Allowed : 11.02 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -1.18 (0.41), residues: 414 helix: -2.41 (0.71), residues: 38 sheet: -0.53 (0.53), residues: 110 loop : -0.60 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 36 HIS 0.000 0.000 HIS A 519 PHE 0.009 0.001 PHE A 515 TYR 0.010 0.001 TYR L 49 ARG 0.002 0.000 ARG H 50 Details of bonding type rmsd link_NAG-ASN : bond 0.00233 ( 1) link_NAG-ASN : angle 1.13577 ( 3) hydrogen bonds : bond 0.28302 ( 82) hydrogen bonds : angle 12.28426 ( 207) SS BOND : bond 0.19373 ( 6) SS BOND : angle 15.41414 ( 12) covalent geometry : bond 0.00329 ( 3349) covalent geometry : angle 0.58682 ( 4547) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 134 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 PHE cc_start: 0.8021 (t80) cc_final: 0.7522 (t80) REVERT: A 368 LEU cc_start: 0.5658 (mm) cc_final: 0.5449 (mm) REVERT: A 403 ARG cc_start: 0.8365 (ttp-170) cc_final: 0.8158 (ttp-110) REVERT: A 458 LYS cc_start: 0.8878 (ttpt) cc_final: 0.8652 (mmtm) REVERT: A 507 PRO cc_start: 0.8330 (Cg_exo) cc_final: 0.8077 (Cg_endo) REVERT: H 10 GLU cc_start: 0.3299 (tt0) cc_final: 0.3026 (mt-10) REVERT: H 29 PHE cc_start: 0.7177 (m-80) cc_final: 0.6948 (m-10) REVERT: H 46 GLU cc_start: 0.7435 (mt-10) cc_final: 0.7202 (mt-10) REVERT: H 79 TYR cc_start: 0.7709 (m-80) cc_final: 0.6961 (m-80) REVERT: L 4 MET cc_start: 0.7409 (mmm) cc_final: 0.6709 (mmm) REVERT: L 18 ARG cc_start: 0.7787 (ttp-170) cc_final: 0.6999 (tpp-160) REVERT: L 36 TYR cc_start: 0.8654 (m-10) cc_final: 0.8420 (m-10) REVERT: L 49 TYR cc_start: 0.8499 (p90) cc_final: 0.8092 (p90) REVERT: L 87 TYR cc_start: 0.8368 (m-80) cc_final: 0.8127 (m-10) outliers start: 9 outliers final: 3 residues processed: 139 average time/residue: 0.2002 time to fit residues: 32.1675 Evaluate side-chains 105 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 102 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain L residue 3 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 16 optimal weight: 0.0020 chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 0.0770 chunk 31 optimal weight: 0.0570 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 overall best weight: 0.3664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 61 GLN ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 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 = 0.3889 r_free = 0.3889 target = 0.140280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.124308 restraints weight = 6953.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.127567 restraints weight = 4033.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.129922 restraints weight = 2738.695| |-----------------------------------------------------------------------------| r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3356 Z= 0.132 Angle : 0.576 5.292 4562 Z= 0.304 Chirality : 0.046 0.162 497 Planarity : 0.006 0.058 589 Dihedral : 4.705 39.162 490 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.80 % Allowed : 16.38 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.90 (0.40), residues: 414 helix: -1.05 (0.91), residues: 31 sheet: -0.00 (0.54), residues: 97 loop : -0.77 (0.36), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 36 HIS 0.000 0.000 HIS A 519 PHE 0.016 0.001 PHE A 464 TYR 0.013 0.001 TYR A 380 ARG 0.004 0.001 ARG L 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00192 ( 1) link_NAG-ASN : angle 1.13321 ( 3) hydrogen bonds : bond 0.04620 ( 82) hydrogen bonds : angle 8.22642 ( 207) SS BOND : bond 0.00292 ( 6) SS BOND : angle 1.05112 ( 12) covalent geometry : bond 0.00294 ( 3349) covalent geometry : angle 0.57343 ( 4547) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 355 ARG cc_start: 0.7833 (ttt90) cc_final: 0.6859 (ttm170) REVERT: A 464 PHE cc_start: 0.6848 (OUTLIER) cc_final: 0.6390 (t80) REVERT: A 474 GLN cc_start: 0.6368 (mt0) cc_final: 0.5891 (mm-40) REVERT: A 507 PRO cc_start: 0.8167 (Cg_exo) cc_final: 0.7884 (Cg_endo) REVERT: H 79 TYR cc_start: 0.7284 (m-80) cc_final: 0.6627 (m-80) REVERT: L 4 MET cc_start: 0.7507 (mmm) cc_final: 0.7144 (tpp) REVERT: L 11 LEU cc_start: 0.7517 (OUTLIER) cc_final: 0.7085 (tm) REVERT: L 18 ARG cc_start: 0.7748 (ttp-170) cc_final: 0.6984 (tpp-160) outliers start: 17 outliers final: 8 residues processed: 113 average time/residue: 0.1943 time to fit residues: 25.4988 Evaluate side-chains 107 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 91 TYR Chi-restraints excluded: chain L residue 96 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 5 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 31 optimal weight: 0.0060 chunk 12 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN H 6 GLN H 61 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 93 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.137823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.121694 restraints weight = 7058.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.124898 restraints weight = 4143.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.127237 restraints weight = 2855.993| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3356 Z= 0.158 Angle : 0.594 6.608 4562 Z= 0.306 Chirality : 0.046 0.178 497 Planarity : 0.005 0.047 589 Dihedral : 4.878 40.950 488 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 5.93 % Allowed : 18.64 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.95 (0.40), residues: 414 helix: -0.88 (0.97), residues: 31 sheet: -0.19 (0.52), residues: 96 loop : -0.76 (0.36), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 353 HIS 0.000 0.000 HIS A 519 PHE 0.016 0.001 PHE A 338 TYR 0.012 0.001 TYR H 47 ARG 0.005 0.000 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00137 ( 1) link_NAG-ASN : angle 1.26316 ( 3) hydrogen bonds : bond 0.03918 ( 82) hydrogen bonds : angle 7.32616 ( 207) SS BOND : bond 0.00240 ( 6) SS BOND : angle 0.80353 ( 12) covalent geometry : bond 0.00357 ( 3349) covalent geometry : angle 0.59298 ( 4547) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 355 ARG cc_start: 0.8261 (ttt90) cc_final: 0.6833 (ttm170) REVERT: A 464 PHE cc_start: 0.6789 (OUTLIER) cc_final: 0.6088 (t80) REVERT: A 474 GLN cc_start: 0.6291 (mt0) cc_final: 0.5822 (mm-40) REVERT: H 79 TYR cc_start: 0.7276 (m-80) cc_final: 0.6681 (m-80) REVERT: L 4 MET cc_start: 0.7553 (mmm) cc_final: 0.6819 (mmm) REVERT: L 11 LEU cc_start: 0.7606 (OUTLIER) cc_final: 0.7129 (tm) REVERT: L 18 ARG cc_start: 0.7765 (ttp-170) cc_final: 0.6917 (tpp-160) outliers start: 21 outliers final: 13 residues processed: 110 average time/residue: 0.1775 time to fit residues: 22.9725 Evaluate side-chains 105 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 96 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 34 optimal weight: 0.1980 chunk 23 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 6 GLN H 61 GLN L 79 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.139793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.123031 restraints weight = 7016.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.126313 restraints weight = 4224.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.128655 restraints weight = 2945.029| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3356 Z= 0.156 Angle : 0.583 5.194 4562 Z= 0.300 Chirality : 0.046 0.189 497 Planarity : 0.005 0.046 589 Dihedral : 4.892 40.346 488 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 7.34 % Allowed : 19.21 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.86 (0.41), residues: 414 helix: -0.71 (1.10), residues: 25 sheet: -0.13 (0.52), residues: 94 loop : -0.71 (0.36), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 36 HIS 0.000 0.000 HIS A 519 PHE 0.006 0.001 PHE L 62 TYR 0.013 0.001 TYR H 47 ARG 0.005 0.000 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00149 ( 1) link_NAG-ASN : angle 1.27302 ( 3) hydrogen bonds : bond 0.03551 ( 82) hydrogen bonds : angle 7.03370 ( 207) SS BOND : bond 0.00262 ( 6) SS BOND : angle 0.74077 ( 12) covalent geometry : bond 0.00352 ( 3349) covalent geometry : angle 0.58161 ( 4547) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 96 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 457 ARG cc_start: 0.7627 (ttt-90) cc_final: 0.7294 (ttt90) REVERT: A 464 PHE cc_start: 0.6615 (OUTLIER) cc_final: 0.6022 (t80) REVERT: H 14 PHE cc_start: 0.7636 (OUTLIER) cc_final: 0.7417 (m-80) REVERT: H 29 PHE cc_start: 0.7105 (m-10) cc_final: 0.6560 (m-10) REVERT: H 79 TYR cc_start: 0.7334 (m-80) cc_final: 0.6698 (m-80) REVERT: H 86 ASP cc_start: 0.7644 (OUTLIER) cc_final: 0.7130 (t70) REVERT: L 4 MET cc_start: 0.7442 (mmm) cc_final: 0.6772 (mmm) REVERT: L 11 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.7109 (tm) REVERT: L 18 ARG cc_start: 0.7737 (ttp-170) cc_final: 0.6896 (tpp-160) outliers start: 26 outliers final: 17 residues processed: 111 average time/residue: 0.1582 time to fit residues: 21.0600 Evaluate side-chains 110 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 89 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 14 PHE Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 96 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 18 optimal weight: 0.7980 chunk 20 optimal weight: 0.0570 chunk 2 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 1 optimal weight: 0.4980 chunk 26 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN H 61 GLN L 79 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.140902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.123889 restraints weight = 7113.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.127202 restraints weight = 4310.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.129527 restraints weight = 3016.115| |-----------------------------------------------------------------------------| r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3356 Z= 0.135 Angle : 0.581 5.441 4562 Z= 0.297 Chirality : 0.046 0.184 497 Planarity : 0.005 0.045 589 Dihedral : 4.853 39.410 488 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 5.93 % Allowed : 22.03 % Favored : 72.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.95 (0.40), residues: 414 helix: -0.22 (1.31), residues: 19 sheet: -0.22 (0.52), residues: 88 loop : -0.82 (0.36), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP H 103 HIS 0.000 0.000 HIS A 519 PHE 0.008 0.001 PHE A 338 TYR 0.011 0.001 TYR A 489 ARG 0.006 0.000 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00222 ( 1) link_NAG-ASN : angle 1.28901 ( 3) hydrogen bonds : bond 0.03349 ( 82) hydrogen bonds : angle 6.84954 ( 207) SS BOND : bond 0.00249 ( 6) SS BOND : angle 0.67370 ( 12) covalent geometry : bond 0.00309 ( 3349) covalent geometry : angle 0.57956 ( 4547) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 93 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: A 338 PHE cc_start: 0.7839 (t80) cc_final: 0.7408 (t80) REVERT: A 457 ARG cc_start: 0.7585 (ttt-90) cc_final: 0.7317 (ttt-90) REVERT: H 14 PHE cc_start: 0.7629 (OUTLIER) cc_final: 0.7401 (m-80) REVERT: H 79 TYR cc_start: 0.7297 (m-80) cc_final: 0.6647 (m-80) REVERT: L 11 LEU cc_start: 0.7654 (OUTLIER) cc_final: 0.7152 (tm) REVERT: L 18 ARG cc_start: 0.7678 (ttp-170) cc_final: 0.6836 (tpp-160) outliers start: 21 outliers final: 15 residues processed: 106 average time/residue: 0.1679 time to fit residues: 21.3149 Evaluate side-chains 103 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 14 PHE Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 91 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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: 57.3228 > 50: distance: 39 - 132: 16.309 distance: 42 - 129: 4.293 distance: 72 - 128: 8.580 distance: 75 - 80: 14.825 distance: 80 - 81: 20.813 distance: 81 - 82: 22.477 distance: 82 - 83: 9.653 distance: 82 - 84: 20.518 distance: 85 - 86: 13.993 distance: 85 - 88: 8.768 distance: 86 - 87: 16.320 distance: 86 - 91: 20.371 distance: 88 - 89: 5.999 distance: 88 - 90: 21.083 distance: 91 - 92: 17.460 distance: 92 - 93: 9.410 distance: 92 - 95: 9.307 distance: 93 - 94: 23.870 distance: 93 - 100: 11.623 distance: 95 - 96: 14.565 distance: 96 - 97: 8.577 distance: 97 - 98: 8.319 distance: 97 - 99: 8.508 distance: 100 - 101: 23.925 distance: 101 - 102: 14.598 distance: 102 - 103: 5.979 distance: 102 - 104: 6.209 distance: 104 - 105: 8.036 distance: 105 - 106: 12.110 distance: 105 - 108: 6.900 distance: 106 - 107: 25.058 distance: 106 - 115: 7.787 distance: 108 - 109: 5.813 distance: 109 - 111: 5.122 distance: 110 - 112: 7.863 distance: 111 - 113: 4.905 distance: 113 - 114: 3.356 distance: 115 - 116: 8.595 distance: 116 - 117: 9.356 distance: 116 - 119: 16.951 distance: 117 - 118: 16.043 distance: 117 - 123: 7.646 distance: 119 - 120: 6.840 distance: 120 - 121: 13.206 distance: 120 - 122: 11.088 distance: 123 - 124: 8.612 distance: 124 - 125: 26.555 distance: 124 - 127: 5.567 distance: 125 - 126: 18.440 distance: 125 - 129: 11.194 distance: 127 - 128: 21.921 distance: 129 - 130: 14.203 distance: 130 - 131: 3.486 distance: 130 - 133: 14.601 distance: 131 - 132: 7.488 distance: 131 - 141: 7.595 distance: 133 - 134: 20.333 distance: 134 - 135: 15.214 distance: 134 - 136: 5.098 distance: 135 - 137: 9.659 distance: 136 - 138: 4.417 distance: 137 - 139: 12.178 distance: 138 - 139: 12.933 distance: 139 - 140: 9.003 distance: 141 - 142: 15.547 distance: 142 - 143: 24.580 distance: 142 - 145: 38.898 distance: 143 - 144: 21.560 distance: 143 - 152: 41.375 distance: 145 - 146: 22.468 distance: 146 - 147: 28.516 distance: 146 - 148: 14.355 distance: 147 - 149: 11.111 distance: 148 - 150: 15.761 distance: 149 - 151: 14.639 distance: 150 - 151: 5.736 distance: 152 - 153: 18.914 distance: 152 - 158: 32.840 distance: 153 - 154: 14.074 distance: 153 - 156: 30.625 distance: 154 - 155: 28.738 distance: 154 - 159: 14.170 distance: 156 - 157: 17.926 distance: 157 - 158: 31.009