Starting phenix.real_space_refine on Tue Feb 11 00:15:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7swp_25478/02_2025/7swp_25478_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7swp_25478/02_2025/7swp_25478.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7swp_25478/02_2025/7swp_25478.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7swp_25478/02_2025/7swp_25478.map" model { file = "/net/cci-nas-00/data/ceres_data/7swp_25478/02_2025/7swp_25478_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7swp_25478/02_2025/7swp_25478_neut.cif" } resolution = 3.8 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 14 5.16 5 C 2137 2.51 5 N 573 2.21 5 O 648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 3372 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1545 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 11, 'TRANS': 183} Chain: "H" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1017 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "L" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 810 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 104} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 2.77, per 1000 atoms: 0.82 Number of scatterers: 3372 At special positions: 0 Unit cell: (84.15, 59.4, 89.1, 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 14 16.00 O 648 8.00 N 573 7.00 C 2137 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=2.03 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=2.04 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 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " 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: 0.80 Conformation dependent library (CDL) restraints added in 386.6 milliseconds 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 782 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 8 sheets defined 15.1% alpha, 32.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 364 through 370 removed outlier: 3.584A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 388 removed outlier: 4.236A pdb=" N ASN A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 409 removed outlier: 3.828A 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 'H' and resid 28 through 32 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 105 through 109 removed outlier: 3.876A pdb=" N TYR H 109 " --> pdb=" O SER H 106 " (cutoff:3.500A) Processing helix chain 'L' and resid 81 through 85 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 356 removed outlier: 3.782A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 453 through 454 Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.547A pdb=" N ASP H 73 " --> pdb=" O THR H 78 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER H 71 " --> pdb=" O TYR H 80 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.687A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AA6, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.623A pdb=" N TRP L 37 " --> pdb=" O LEU L 49 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 9 through 12 Processing sheet with id=AA8, first strand: chain 'L' and resid 17 through 23 119 hydrogen bonds defined for protein. 273 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: 0.99 Time building geometry restraints manager: 0.94 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: 1087 1.34 - 1.46: 924 1.46 - 1.58: 1434 1.58 - 1.71: 0 1.71 - 1.83: 16 Bond restraints: 3461 Sorted by residual: bond pdb=" C TYR A 421 " pdb=" N ASN A 422 " ideal model delta sigma weight residual 1.332 1.282 0.050 1.40e-02 5.10e+03 1.27e+01 bond pdb=" C LYS A 424 " pdb=" N LEU A 425 " ideal model delta sigma weight residual 1.331 1.233 0.098 2.83e-02 1.25e+03 1.19e+01 bond pdb=" N VAL L 100 " pdb=" CA VAL L 100 " ideal model delta sigma weight residual 1.458 1.495 -0.036 1.21e-02 6.83e+03 8.88e+00 bond pdb=" N VAL L 101 " pdb=" CA VAL L 101 " ideal model delta sigma weight residual 1.458 1.493 -0.036 1.24e-02 6.50e+03 8.21e+00 bond pdb=" N THR L 106 " pdb=" CA THR L 106 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.21e-02 6.83e+03 6.96e+00 ... (remaining 3456 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 4371 1.61 - 3.21: 276 3.21 - 4.82: 43 4.82 - 6.42: 12 6.42 - 8.03: 5 Bond angle restraints: 4707 Sorted by residual: angle pdb=" C HIS L 36 " pdb=" N TRP L 37 " pdb=" CA TRP L 37 " ideal model delta sigma weight residual 122.94 115.73 7.21 1.50e+00 4.44e-01 2.31e+01 angle pdb=" C TYR A 421 " pdb=" N ASN A 422 " pdb=" CA ASN A 422 " ideal model delta sigma weight residual 121.54 113.51 8.03 1.91e+00 2.74e-01 1.77e+01 angle pdb=" C PRO A 527 " pdb=" N LYS A 528 " pdb=" CA LYS A 528 " ideal model delta sigma weight residual 121.70 127.24 -5.54 1.80e+00 3.09e-01 9.48e+00 angle pdb=" N GLY A 526 " pdb=" CA GLY A 526 " pdb=" C GLY A 526 " ideal model delta sigma weight residual 112.34 118.59 -6.25 2.04e+00 2.40e-01 9.38e+00 angle pdb=" CA GLY L 103 " pdb=" C GLY L 103 " pdb=" O GLY L 103 " ideal model delta sigma weight residual 122.24 118.32 3.92 1.30e+00 5.92e-01 9.10e+00 ... (remaining 4702 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 1840 17.57 - 35.15: 163 35.15 - 52.72: 15 52.72 - 70.29: 4 70.29 - 87.87: 2 Dihedral angle restraints: 2024 sinusoidal: 776 harmonic: 1248 Sorted by residual: dihedral pdb=" CA CYS A 391 " pdb=" C CYS A 391 " pdb=" N PHE A 392 " pdb=" CA PHE A 392 " ideal model delta harmonic sigma weight residual -180.00 -151.49 -28.51 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 46.90 46.10 1 1.00e+01 1.00e-02 2.94e+01 dihedral pdb=" CA SER A 477 " pdb=" C SER A 477 " pdb=" N THR A 478 " pdb=" CA THR A 478 " ideal model delta harmonic sigma weight residual -180.00 -157.35 -22.65 0 5.00e+00 4.00e-02 2.05e+01 ... (remaining 2021 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 354 0.048 - 0.096: 103 0.096 - 0.145: 33 0.145 - 0.193: 3 0.193 - 0.241: 2 Chirality restraints: 495 Sorted by residual: chirality pdb=" CB ILE L 50 " pdb=" CA ILE L 50 " pdb=" CG1 ILE L 50 " pdb=" CG2 ILE L 50 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CG LEU H 81 " pdb=" CB LEU H 81 " pdb=" CD1 LEU H 81 " pdb=" CD2 LEU H 81 " both_signs ideal model delta sigma weight residual False -2.59 -2.80 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA VAL L 101 " pdb=" N VAL L 101 " pdb=" C VAL L 101 " pdb=" CB VAL L 101 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 6.86e-01 ... (remaining 492 not shown) Planarity restraints: 617 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP L 37 " -0.035 2.00e-02 2.50e+03 4.40e-02 4.85e+01 pdb=" CG TRP L 37 " 0.109 2.00e-02 2.50e+03 pdb=" CD1 TRP L 37 " -0.074 2.00e-02 2.50e+03 pdb=" CD2 TRP L 37 " 0.009 2.00e-02 2.50e+03 pdb=" NE1 TRP L 37 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TRP L 37 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP L 37 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 37 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 37 " -0.023 2.00e-02 2.50e+03 pdb=" CH2 TRP L 37 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 526 " 0.037 5.00e-02 4.00e+02 5.62e-02 5.05e+00 pdb=" N PRO A 527 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 527 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 527 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 453 " 0.007 2.00e-02 2.50e+03 1.47e-02 2.16e+00 pdb=" C TYR A 453 " -0.025 2.00e-02 2.50e+03 pdb=" O TYR A 453 " 0.010 2.00e-02 2.50e+03 pdb=" N ARG A 454 " 0.009 2.00e-02 2.50e+03 ... (remaining 614 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 569 2.74 - 3.28: 3775 3.28 - 3.82: 6048 3.82 - 4.36: 7001 4.36 - 4.90: 11348 Nonbonded interactions: 28741 Sorted by model distance: nonbonded pdb=" OD2 ASP L 94 " pdb=" OG SER L 96 " model vdw 2.202 3.040 nonbonded pdb=" NE2 GLN H 13 " pdb=" O SER H 128 " model vdw 2.206 3.120 nonbonded pdb=" O TYR H 53 " pdb=" NH2 ARG H 72 " model vdw 2.214 3.120 nonbonded pdb=" OG1 THR A 415 " pdb=" OG SER L 58 " model vdw 2.216 3.040 nonbonded pdb=" O LYS A 444 " pdb=" NE2 GLN A 498 " model vdw 2.224 3.120 ... (remaining 28736 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.720 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.930 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:3.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 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 : 0.008 0.098 3461 Z= 0.534 Angle : 0.925 8.029 4707 Z= 0.525 Chirality : 0.051 0.241 495 Planarity : 0.006 0.056 617 Dihedral : 12.869 87.868 1224 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 40.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.09 % Favored : 87.91 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.38), residues: 430 helix: -3.11 (0.87), residues: 21 sheet: -1.11 (0.44), residues: 122 loop : -1.50 (0.36), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.109 0.006 TRP L 37 HIS 0.007 0.003 HIS L 36 PHE 0.023 0.002 PHE A 490 TYR 0.021 0.003 TYR L 51 ARG 0.011 0.001 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 GLU cc_start: 0.8499 (tm-30) cc_final: 0.8298 (tm-30) REVERT: A 356 LYS cc_start: 0.8283 (tppt) cc_final: 0.7661 (tptt) REVERT: A 398 ASP cc_start: 0.7717 (m-30) cc_final: 0.7370 (m-30) REVERT: A 403 ARG cc_start: 0.6932 (ptt90) cc_final: 0.6642 (ptt90) REVERT: A 501 ASN cc_start: 0.7847 (t0) cc_final: 0.7428 (t0) REVERT: A 517 LEU cc_start: 0.8767 (mt) cc_final: 0.8271 (tt) REVERT: H 2 VAL cc_start: 0.7845 (m) cc_final: 0.7345 (m) REVERT: H 16 ARG cc_start: 0.5405 (ptt-90) cc_final: 0.5174 (ptp-110) REVERT: H 34 MET cc_start: 0.8260 (mmp) cc_final: 0.8041 (mmm) REVERT: H 35 GLN cc_start: 0.8219 (mp10) cc_final: 0.7931 (mp10) REVERT: H 95 TYR cc_start: 0.7581 (m-80) cc_final: 0.7352 (m-80) REVERT: H 105 ASP cc_start: 0.8435 (t70) cc_final: 0.7971 (t70) REVERT: H 111 GLN cc_start: 0.8031 (mm-40) cc_final: 0.7824 (mp10) REVERT: H 112 THR cc_start: 0.8451 (p) cc_final: 0.8147 (m) REVERT: L 34 ASP cc_start: 0.7296 (p0) cc_final: 0.6964 (p0) REVERT: L 87 ASP cc_start: 0.7942 (p0) cc_final: 0.7573 (t70) REVERT: L 101 VAL cc_start: 0.8380 (t) cc_final: 0.8081 (t) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.2058 time to fit residues: 38.4135 Evaluate side-chains 98 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 8.9990 chunk 31 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 117 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 = 0.3896 r_free = 0.3896 target = 0.122310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.105797 restraints weight = 9044.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.109283 restraints weight = 4803.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.111610 restraints weight = 3097.990| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3461 Z= 0.259 Angle : 0.786 8.991 4707 Z= 0.403 Chirality : 0.050 0.140 495 Planarity : 0.006 0.040 617 Dihedral : 5.759 25.006 487 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 17.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 3.02 % Allowed : 13.46 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.38), residues: 430 helix: -3.53 (0.68), residues: 22 sheet: -0.73 (0.44), residues: 132 loop : -1.23 (0.35), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP L 37 HIS 0.006 0.002 HIS A 519 PHE 0.018 0.002 PHE H 27 TYR 0.022 0.002 TYR A 365 ARG 0.008 0.001 ARG L 63 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 135 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 356 LYS cc_start: 0.8469 (tppt) cc_final: 0.7863 (tptt) REVERT: A 365 TYR cc_start: 0.8003 (m-80) cc_final: 0.7710 (m-80) REVERT: A 398 ASP cc_start: 0.8217 (m-30) cc_final: 0.7942 (m-30) REVERT: A 403 ARG cc_start: 0.7511 (ptt90) cc_final: 0.6508 (ptt90) REVERT: A 406 GLU cc_start: 0.8681 (pm20) cc_final: 0.7945 (pm20) REVERT: A 467 ASP cc_start: 0.7732 (OUTLIER) cc_final: 0.6833 (p0) REVERT: A 493 GLN cc_start: 0.8048 (tp40) cc_final: 0.7838 (tp40) REVERT: H 35 GLN cc_start: 0.8170 (mp10) cc_final: 0.7818 (mp10) REVERT: H 95 TYR cc_start: 0.7159 (m-80) cc_final: 0.6951 (m-80) REVERT: H 105 ASP cc_start: 0.8433 (t70) cc_final: 0.7824 (t70) REVERT: L 38 TYR cc_start: 0.7439 (m-80) cc_final: 0.7051 (m-80) REVERT: L 89 TYR cc_start: 0.7805 (m-80) cc_final: 0.7476 (m-10) REVERT: L 101 VAL cc_start: 0.8715 (t) cc_final: 0.8476 (p) outliers start: 11 outliers final: 7 residues processed: 139 average time/residue: 0.1728 time to fit residues: 28.5483 Evaluate side-chains 113 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 105 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 80 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 23 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 30 optimal weight: 4.9990 chunk 11 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.117868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.100790 restraints weight = 9032.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.104166 restraints weight = 4925.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.106409 restraints weight = 3234.387| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.4791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 3461 Z= 0.344 Angle : 0.782 8.500 4707 Z= 0.408 Chirality : 0.049 0.176 495 Planarity : 0.006 0.052 617 Dihedral : 5.793 26.482 487 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 20.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 6.59 % Allowed : 15.38 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.37), residues: 430 helix: -3.36 (0.76), residues: 22 sheet: -0.62 (0.44), residues: 121 loop : -1.31 (0.35), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.004 TRP L 37 HIS 0.006 0.003 HIS L 36 PHE 0.021 0.002 PHE A 392 TYR 0.027 0.003 TYR A 351 ARG 0.006 0.001 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 107 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 LYS cc_start: 0.8481 (tppt) cc_final: 0.7916 (tptt) REVERT: A 365 TYR cc_start: 0.8205 (OUTLIER) cc_final: 0.7918 (m-80) REVERT: A 389 ASP cc_start: 0.9072 (t0) cc_final: 0.8684 (t0) REVERT: A 398 ASP cc_start: 0.8475 (m-30) cc_final: 0.8208 (m-30) REVERT: A 401 VAL cc_start: 0.8996 (OUTLIER) cc_final: 0.8769 (t) REVERT: A 406 GLU cc_start: 0.9093 (pm20) cc_final: 0.8488 (pm20) REVERT: A 487 ASN cc_start: 0.6838 (t0) cc_final: 0.6571 (t0) REVERT: H 2 VAL cc_start: 0.7987 (m) cc_final: 0.7675 (p) REVERT: H 34 MET cc_start: 0.8177 (mmm) cc_final: 0.7841 (mmt) REVERT: H 35 GLN cc_start: 0.8262 (mp10) cc_final: 0.7998 (mp10) REVERT: H 47 TRP cc_start: 0.8038 (t60) cc_final: 0.7778 (t60) REVERT: L 20 ILE cc_start: 0.8819 (mp) cc_final: 0.8611 (mt) REVERT: L 51 TYR cc_start: 0.8416 (p90) cc_final: 0.8144 (p90) REVERT: L 85 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7486 (mm-30) REVERT: L 101 VAL cc_start: 0.8799 (t) cc_final: 0.8519 (p) outliers start: 24 outliers final: 15 residues processed: 121 average time/residue: 0.1355 time to fit residues: 20.3376 Evaluate side-chains 123 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 74 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 12 optimal weight: 8.9990 chunk 25 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 39 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 11 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN L 28 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.119162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.102136 restraints weight = 9110.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.105559 restraints weight = 4967.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.107801 restraints weight = 3235.008| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.5389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3461 Z= 0.258 Angle : 0.741 9.565 4707 Z= 0.381 Chirality : 0.048 0.172 495 Planarity : 0.005 0.042 617 Dihedral : 5.368 24.823 487 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 6.32 % Allowed : 18.68 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.38), residues: 430 helix: -3.15 (0.77), residues: 22 sheet: -0.51 (0.43), residues: 131 loop : -1.13 (0.36), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.003 TRP L 37 HIS 0.005 0.002 HIS L 36 PHE 0.021 0.002 PHE A 392 TYR 0.025 0.002 TYR A 351 ARG 0.006 0.001 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 112 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 LYS cc_start: 0.8581 (tppt) cc_final: 0.8031 (tptt) REVERT: A 389 ASP cc_start: 0.9116 (t0) cc_final: 0.8740 (t0) REVERT: A 401 VAL cc_start: 0.8963 (t) cc_final: 0.8734 (t) REVERT: A 417 LYS cc_start: 0.8898 (tppt) cc_final: 0.8501 (tppt) REVERT: H 2 VAL cc_start: 0.8045 (m) cc_final: 0.7815 (p) REVERT: H 19 ARG cc_start: 0.7478 (ttt180) cc_final: 0.7152 (tpt-90) REVERT: H 47 TRP cc_start: 0.7963 (t60) cc_final: 0.7681 (t60) REVERT: H 59 TYR cc_start: 0.8171 (m-80) cc_final: 0.7932 (m-80) REVERT: H 95 TYR cc_start: 0.7376 (m-80) cc_final: 0.7070 (m-80) REVERT: L 36 HIS cc_start: 0.8940 (OUTLIER) cc_final: 0.8226 (m-70) REVERT: L 51 TYR cc_start: 0.8413 (p90) cc_final: 0.8129 (p90) REVERT: L 97 LEU cc_start: 0.7947 (mp) cc_final: 0.7726 (tt) REVERT: L 101 VAL cc_start: 0.8763 (t) cc_final: 0.8464 (p) outliers start: 23 outliers final: 16 residues processed: 126 average time/residue: 0.1416 time to fit residues: 21.9890 Evaluate side-chains 119 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 36 HIS Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 74 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 13 optimal weight: 0.2980 chunk 39 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 2 optimal weight: 8.9990 chunk 11 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 17 optimal weight: 8.9990 chunk 22 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 overall best weight: 4.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 13 GLN L 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.115125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.097417 restraints weight = 9246.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.100734 restraints weight = 5077.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.102963 restraints weight = 3366.659| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.6195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 3461 Z= 0.385 Angle : 0.778 10.088 4707 Z= 0.411 Chirality : 0.049 0.161 495 Planarity : 0.006 0.059 617 Dihedral : 5.873 26.336 487 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 19.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.53 % Favored : 90.47 % Rotamer: Outliers : 7.42 % Allowed : 19.51 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.39), residues: 430 helix: -2.71 (0.85), residues: 28 sheet: -0.33 (0.44), residues: 121 loop : -1.20 (0.37), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP L 37 HIS 0.006 0.003 HIS L 36 PHE 0.024 0.002 PHE A 392 TYR 0.024 0.002 TYR A 369 ARG 0.006 0.001 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 110 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 356 LYS cc_start: 0.8509 (tppt) cc_final: 0.7949 (tptt) REVERT: A 365 TYR cc_start: 0.8248 (OUTLIER) cc_final: 0.7869 (m-80) REVERT: A 389 ASP cc_start: 0.9285 (t0) cc_final: 0.9059 (t0) REVERT: A 406 GLU cc_start: 0.9250 (pm20) cc_final: 0.8719 (pm20) REVERT: A 414 GLN cc_start: 0.8603 (mp-120) cc_final: 0.8255 (mp10) REVERT: A 421 TYR cc_start: 0.8787 (m-10) cc_final: 0.8547 (m-10) REVERT: A 461 LEU cc_start: 0.8750 (tp) cc_final: 0.8469 (tp) REVERT: A 493 GLN cc_start: 0.8027 (tp40) cc_final: 0.7787 (tp40) REVERT: H 2 VAL cc_start: 0.8289 (m) cc_final: 0.7961 (p) REVERT: H 95 TYR cc_start: 0.7327 (m-80) cc_final: 0.7034 (m-80) REVERT: L 34 ASP cc_start: 0.6707 (p0) cc_final: 0.6453 (p0) REVERT: L 36 HIS cc_start: 0.8851 (OUTLIER) cc_final: 0.8446 (m-70) REVERT: L 51 TYR cc_start: 0.8589 (p90) cc_final: 0.8270 (p90) REVERT: L 81 GLN cc_start: 0.8309 (tm-30) cc_final: 0.7741 (tt0) REVERT: L 101 VAL cc_start: 0.8752 (t) cc_final: 0.8468 (p) outliers start: 27 outliers final: 21 residues processed: 127 average time/residue: 0.1376 time to fit residues: 21.7567 Evaluate side-chains 124 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 36 HIS Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 74 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 17 optimal weight: 8.9990 chunk 7 optimal weight: 0.4980 chunk 18 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 chunk 31 optimal weight: 0.2980 chunk 27 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.118987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.101476 restraints weight = 9031.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.104877 restraints weight = 4852.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.107241 restraints weight = 3174.424| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.6457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3461 Z= 0.199 Angle : 0.746 11.215 4707 Z= 0.373 Chirality : 0.047 0.164 495 Planarity : 0.005 0.040 617 Dihedral : 5.175 22.809 487 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 7.42 % Allowed : 21.43 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.39), residues: 430 helix: -2.83 (0.84), residues: 22 sheet: -0.27 (0.44), residues: 132 loop : -0.87 (0.37), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP L 37 HIS 0.005 0.002 HIS L 36 PHE 0.020 0.002 PHE A 338 TYR 0.022 0.002 TYR A 351 ARG 0.004 0.001 ARG H 31 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 110 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 LYS cc_start: 0.8477 (tppt) cc_final: 0.8001 (tptt) REVERT: A 389 ASP cc_start: 0.9290 (t0) cc_final: 0.9055 (t0) REVERT: A 401 VAL cc_start: 0.9010 (t) cc_final: 0.8805 (t) REVERT: A 406 GLU cc_start: 0.9025 (pm20) cc_final: 0.8547 (pm20) REVERT: A 417 LYS cc_start: 0.9082 (tppt) cc_final: 0.8872 (tppt) REVERT: A 493 GLN cc_start: 0.7982 (tp40) cc_final: 0.7732 (tp40) REVERT: H 1 GLN cc_start: 0.8456 (tt0) cc_final: 0.8171 (tp40) REVERT: H 2 VAL cc_start: 0.8267 (m) cc_final: 0.7940 (p) REVERT: H 3 GLN cc_start: 0.7286 (pm20) cc_final: 0.7055 (pm20) REVERT: H 95 TYR cc_start: 0.7390 (m-80) cc_final: 0.7035 (m-80) REVERT: H 117 GLN cc_start: 0.8624 (OUTLIER) cc_final: 0.8006 (mt0) REVERT: L 36 HIS cc_start: 0.8991 (OUTLIER) cc_final: 0.8203 (m-70) REVERT: L 51 TYR cc_start: 0.8333 (p90) cc_final: 0.7977 (p90) REVERT: L 81 GLN cc_start: 0.8325 (tm-30) cc_final: 0.7842 (tt0) REVERT: L 97 LEU cc_start: 0.8078 (mp) cc_final: 0.7853 (tt) REVERT: L 100 VAL cc_start: 0.7962 (p) cc_final: 0.7674 (p) REVERT: L 101 VAL cc_start: 0.8645 (t) cc_final: 0.8415 (p) outliers start: 27 outliers final: 20 residues processed: 127 average time/residue: 0.1389 time to fit residues: 21.9940 Evaluate side-chains 124 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 116 PHE Chi-restraints excluded: chain H residue 117 GLN Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 36 HIS Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 74 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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-5592/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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-5592/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-5592/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-5592/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-5592/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-5592/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-5592/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-5592/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-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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-5592/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-5592/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-5592/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-5592/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: 70.9972 > 50: distance: 21 - 27: 34.237 distance: 28 - 29: 56.689 distance: 28 - 31: 40.917 distance: 29 - 30: 22.081 distance: 29 - 39: 35.794 distance: 32 - 33: 21.566 distance: 32 - 34: 54.309 distance: 33 - 35: 41.495 distance: 34 - 36: 51.578 distance: 35 - 37: 8.844 distance: 36 - 37: 19.102 distance: 37 - 38: 22.186 distance: 39 - 40: 53.206 distance: 40 - 43: 21.673 distance: 41 - 48: 40.629 distance: 43 - 44: 37.552 distance: 44 - 45: 38.633 distance: 45 - 46: 28.544 distance: 45 - 47: 37.134 distance: 49 - 50: 56.478 distance: 49 - 52: 14.795 distance: 50 - 53: 39.080 distance: 53 - 54: 39.122 distance: 54 - 55: 41.551 distance: 55 - 56: 69.041 distance: 58 - 59: 40.579 distance: 58 - 61: 39.814 distance: 59 - 60: 56.181 distance: 59 - 63: 56.161 distance: 61 - 62: 39.608 distance: 63 - 64: 50.462 distance: 64 - 65: 30.344 distance: 64 - 67: 64.881 distance: 65 - 70: 39.428 distance: 67 - 68: 41.302 distance: 70 - 71: 57.150 distance: 70 - 76: 56.665 distance: 71 - 72: 14.013 distance: 72 - 73: 42.993 distance: 72 - 77: 25.780 distance: 77 - 78: 41.177 distance: 78 - 79: 40.271 distance: 78 - 81: 39.552 distance: 79 - 80: 64.214 distance: 79 - 83: 19.685 distance: 81 - 82: 39.759 distance: 82 - 115: 33.211 distance: 83 - 84: 39.678 distance: 84 - 85: 33.484 distance: 84 - 87: 57.857 distance: 85 - 86: 42.630 distance: 85 - 91: 40.988 distance: 87 - 88: 41.255 distance: 88 - 89: 17.083 distance: 88 - 90: 21.560 distance: 91 - 92: 41.520 distance: 92 - 93: 57.154 distance: 93 - 94: 34.135 distance: 93 - 95: 32.298