Starting phenix.real_space_refine on Wed Sep 17 02:58:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6rju_4906/09_2025/6rju_4906.cif Found real_map, /net/cci-nas-00/data/ceres_data/6rju_4906/09_2025/6rju_4906.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6rju_4906/09_2025/6rju_4906.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6rju_4906/09_2025/6rju_4906.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6rju_4906/09_2025/6rju_4906.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6rju_4906/09_2025/6rju_4906.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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: 6 Type Number sf(0) Gaussians Se 3 7.20 5 S 1 5.16 5 C 625 2.51 5 N 178 2.21 5 O 188 1.98 5 H 997 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 1992 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1992 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 3, 'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 23 Time building chain proxies: 0.53, per 1000 atoms: 0.27 Number of scatterers: 1992 At special positions: 0 Unit cell: (57.132, 40.204, 83.582, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Se 3 33.99 S 1 16.00 O 188 8.00 N 178 7.00 C 625 6.00 H 997 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.10 Conformation dependent library (CDL) restraints added in 29.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 254 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 0 sheets defined 72.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.03 Creating SS restraints... Processing helix chain 'A' and resid 404 through 406 No H-bonds generated for 'chain 'A' and resid 404 through 406' Processing helix chain 'A' and resid 407 through 412 removed outlier: 3.613A pdb=" N ASP A 412 " --> pdb=" O LEU A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 425 removed outlier: 3.590A pdb=" N LEU A 420 " --> pdb=" O THR A 416 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN A 424 " --> pdb=" O LEU A 420 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA A 425 " --> pdb=" O SER A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 449 removed outlier: 4.511A pdb=" N ARG A 439 " --> pdb=" O ASN A 435 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU A 440 " --> pdb=" O TRP A 436 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR A 449 " --> pdb=" O VAL A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 467 removed outlier: 4.019A pdb=" N HIS A 457 " --> pdb=" O ASP A 453 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ARG A 465 " --> pdb=" O GLU A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 494 removed outlier: 3.674A pdb=" N VAL A 479 " --> pdb=" O GLU A 475 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU A 481 " --> pdb=" O GLU A 477 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG A 485 " --> pdb=" O GLU A 481 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU A 490 " --> pdb=" O ARG A 486 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG A 491 " --> pdb=" O LEU A 487 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N MSE A 492 " --> pdb=" O LYS A 488 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS A 493 " --> pdb=" O LEU A 489 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N SER A 494 " --> pdb=" O LEU A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 510 Processing helix chain 'A' and resid 510 through 517 removed outlier: 4.037A pdb=" N ILE A 516 " --> pdb=" O LEU A 512 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA A 517 " --> pdb=" O ALA A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 526 removed outlier: 3.626A pdb=" N ALA A 524 " --> pdb=" O ALA A 521 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL A 525 " --> pdb=" O ARG A 522 " (cutoff:3.500A) 40 hydrogen bonds defined for protein. 117 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: 0.20 Time building geometry restraints manager: 0.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.06: 996 1.06 - 1.29: 177 1.29 - 1.51: 452 1.51 - 1.73: 372 1.73 - 1.96: 7 Bond restraints: 2004 Sorted by residual: bond pdb=" CB ASN A 452 " pdb=" CG ASN A 452 " ideal model delta sigma weight residual 1.516 1.565 -0.049 2.50e-02 1.60e+03 3.90e+00 bond pdb=" CG GLU A 461 " pdb=" CD GLU A 461 " ideal model delta sigma weight residual 1.516 1.559 -0.043 2.50e-02 1.60e+03 2.99e+00 bond pdb=" CB GLU A 461 " pdb=" CG GLU A 461 " ideal model delta sigma weight residual 1.520 1.568 -0.048 3.00e-02 1.11e+03 2.56e+00 bond pdb=" CA ASN A 452 " pdb=" CB ASN A 452 " ideal model delta sigma weight residual 1.532 1.553 -0.021 1.51e-02 4.39e+03 1.90e+00 bond pdb=" CB TRP A 474 " pdb=" CG TRP A 474 " ideal model delta sigma weight residual 1.498 1.459 0.039 3.10e-02 1.04e+03 1.61e+00 ... (remaining 1999 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 2949 1.32 - 2.64: 411 2.64 - 3.96: 247 3.96 - 5.28: 23 5.28 - 6.60: 8 Bond angle restraints: 3638 Sorted by residual: angle pdb=" C LYS A 451 " pdb=" N ASN A 452 " pdb=" CA ASN A 452 " ideal model delta sigma weight residual 122.61 128.50 -5.89 1.56e+00 4.11e-01 1.42e+01 angle pdb=" CA ASN A 452 " pdb=" CB ASN A 452 " pdb=" CG ASN A 452 " ideal model delta sigma weight residual 112.60 116.37 -3.77 1.00e+00 1.00e+00 1.42e+01 angle pdb=" N MSE A 492 " pdb=" CA MSE A 492 " pdb=" C MSE A 492 " ideal model delta sigma weight residual 114.04 111.04 3.00 1.24e+00 6.50e-01 5.87e+00 angle pdb=" CA GLN A 505 " pdb=" C GLN A 505 " pdb=" N PRO A 506 " ideal model delta sigma weight residual 118.44 122.27 -3.83 1.59e+00 3.96e-01 5.82e+00 angle pdb=" N ASN A 452 " pdb=" CA ASN A 452 " pdb=" C ASN A 452 " ideal model delta sigma weight residual 112.47 115.25 -2.78 1.24e+00 6.50e-01 5.04e+00 ... (remaining 3633 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.29: 817 16.29 - 32.59: 73 32.59 - 48.88: 19 48.88 - 65.17: 11 65.17 - 81.47: 2 Dihedral angle restraints: 922 sinusoidal: 509 harmonic: 413 Sorted by residual: dihedral pdb=" CA LEU A 469 " pdb=" C LEU A 469 " pdb=" N THR A 470 " pdb=" CA THR A 470 " ideal model delta harmonic sigma weight residual -180.00 -160.06 -19.94 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA THR A 470 " pdb=" C THR A 470 " pdb=" N LEU A 471 " pdb=" CA LEU A 471 " ideal model delta harmonic sigma weight residual 180.00 -160.31 -19.69 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA THR A 449 " pdb=" C THR A 449 " pdb=" N GLY A 450 " pdb=" CA GLY A 450 " ideal model delta harmonic sigma weight residual 180.00 -161.97 -18.03 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 919 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 111 0.046 - 0.092: 46 0.092 - 0.137: 7 0.137 - 0.183: 0 0.183 - 0.229: 1 Chirality restraints: 165 Sorted by residual: chirality pdb=" CA ASN A 452 " pdb=" N ASN A 452 " pdb=" C ASN A 452 " pdb=" CB ASN A 452 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA GLN A 505 " pdb=" N GLN A 505 " pdb=" C GLN A 505 " pdb=" CB GLN A 505 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.86e-01 chirality pdb=" CA ASN A 413 " pdb=" N ASN A 413 " pdb=" C ASN A 413 " pdb=" CB ASN A 413 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 3.17e-01 ... (remaining 162 not shown) Planarity restraints: 302 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 505 " -0.031 5.00e-02 4.00e+02 4.67e-02 3.49e+00 pdb=" N PRO A 506 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 506 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 506 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 451 " 0.007 2.00e-02 2.50e+03 1.51e-02 2.28e+00 pdb=" C LYS A 451 " -0.026 2.00e-02 2.50e+03 pdb=" O LYS A 451 " 0.010 2.00e-02 2.50e+03 pdb=" N ASN A 452 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 474 " -0.002 2.00e-02 2.50e+03 6.48e-03 1.68e+00 pdb=" CG TRP A 474 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TRP A 474 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TRP A 474 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 474 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 474 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 474 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 474 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 474 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 474 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 TRP A 474 " -0.016 2.00e-02 2.50e+03 pdb=" HE1 TRP A 474 " 0.003 2.00e-02 2.50e+03 pdb=" HE3 TRP A 474 " -0.000 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 474 " 0.003 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 474 " -0.004 2.00e-02 2.50e+03 pdb=" HH2 TRP A 474 " -0.002 2.00e-02 2.50e+03 ... (remaining 299 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.33: 400 2.33 - 2.94: 4685 2.94 - 3.56: 4919 3.56 - 4.18: 6409 4.18 - 4.80: 9891 Nonbonded interactions: 26304 Sorted by model distance: nonbonded pdb=" H VAL A 502 " pdb="HG22 VAL A 502 " model vdw 1.708 2.270 nonbonded pdb=" HA ARG A 468 " pdb=" HD2 ARG A 468 " model vdw 1.721 2.440 nonbonded pdb=" OG SER A 494 " pdb=" H ALA A 495 " model vdw 1.776 2.450 nonbonded pdb=" O THR A 497 " pdb=" HG1 THR A 497 " model vdw 1.783 2.450 nonbonded pdb=" H ILE A 516 " pdb="HG13 ILE A 516 " model vdw 1.796 2.270 ... (remaining 26299 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.760 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: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 3.140 Find NCS groups from input model: 0.000 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:0.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 5.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: -0.0287 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 1007 Z= 0.324 Angle : 0.941 6.431 1366 Z= 0.530 Chirality : 0.049 0.229 165 Planarity : 0.005 0.047 176 Dihedral : 15.358 81.468 373 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.63 % Favored : 88.37 % Rotamer: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -7.10 (0.41), residues: 129 helix: -4.88 (0.19), residues: 79 sheet: None (None), residues: 0 loop : -4.14 (0.69), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 522 PHE 0.011 0.004 PHE A 480 TRP 0.016 0.002 TRP A 474 HIS 0.003 0.001 HIS A 457 Details of bonding type rmsd covalent geometry : bond 0.00711 ( 1007) covalent geometry : angle 0.94143 ( 1366) hydrogen bonds : bond 0.31018 ( 40) hydrogen bonds : angle 10.11500 ( 117) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 400 is missing expected H atoms. Skipping. Residue LEU 401 is missing expected H atoms. Skipping. Residue SER 472 is missing expected H atoms. Skipping. Residue LYS 496 is missing expected H atoms. Skipping. Evaluate side-chains 13 residues out of total 109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.2003 time to fit residues: 2.7551 Evaluate side-chains 8 residues out of total 109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 6 optimal weight: 0.7980 chunk 12 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 0.4980 chunk 8 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 5 optimal weight: 0.4980 chunk 9 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 2 optimal weight: 0.0570 chunk 1 optimal weight: 0.4980 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5100 r_free = 0.5100 target = 0.194159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4908 r_free = 0.4908 target = 0.164122 restraints weight = 8031.005| |-----------------------------------------------------------------------------| r_work (start): 0.4954 rms_B_bonded: 11.30 r_work: 0.4757 rms_B_bonded: 10.63 restraints_weight: 2.0000 r_work: 0.4854 rms_B_bonded: 5.93 restraints_weight: 4.0000 r_work (final): 0.4854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0033 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 1007 Z= 0.126 Angle : 0.626 5.598 1366 Z= 0.321 Chirality : 0.032 0.094 165 Planarity : 0.003 0.024 176 Dihedral : 5.809 15.493 139 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 2.02 % Allowed : 9.09 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.64 (0.51), residues: 129 helix: -3.42 (0.38), residues: 84 sheet: None (None), residues: 0 loop : -4.10 (0.70), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 468 PHE 0.003 0.001 PHE A 480 TRP 0.003 0.001 TRP A 474 HIS 0.006 0.002 HIS A 457 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 1007) covalent geometry : angle 0.62569 ( 1366) hydrogen bonds : bond 0.05123 ( 40) hydrogen bonds : angle 5.44102 ( 117) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 400 is missing expected H atoms. Skipping. Residue LEU 401 is missing expected H atoms. Skipping. Residue SER 472 is missing expected H atoms. Skipping. Residue LYS 496 is missing expected H atoms. Skipping. Evaluate side-chains 11 residues out of total 109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 9 time to evaluate : 0.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 10 average time/residue: 0.2505 time to fit residues: 2.6935 Evaluate side-chains 9 residues out of total 109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 0 optimal weight: 9.9990 chunk 6 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 7 optimal weight: 0.0980 chunk 1 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5090 r_free = 0.5090 target = 0.197479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4905 r_free = 0.4905 target = 0.167234 restraints weight = 8069.497| |-----------------------------------------------------------------------------| r_work (start): 0.4969 rms_B_bonded: 11.72 r_work: 0.4714 rms_B_bonded: 11.08 restraints_weight: 2.0000 r_work: 0.4830 rms_B_bonded: 6.48 restraints_weight: 4.0000 r_work (final): 0.4830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0230 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 1007 Z= 0.117 Angle : 0.591 4.333 1366 Z= 0.296 Chirality : 0.030 0.094 165 Planarity : 0.003 0.025 176 Dihedral : 4.698 12.612 139 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.01 % Allowed : 13.13 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.18 (0.65), residues: 129 helix: -2.37 (0.49), residues: 88 sheet: None (None), residues: 0 loop : -3.36 (0.87), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 444 PHE 0.005 0.002 PHE A 480 TRP 0.005 0.001 TRP A 422 HIS 0.004 0.002 HIS A 457 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 1007) covalent geometry : angle 0.59123 ( 1366) hydrogen bonds : bond 0.03483 ( 40) hydrogen bonds : angle 4.31981 ( 117) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 400 is missing expected H atoms. Skipping. Residue LEU 401 is missing expected H atoms. Skipping. Residue SER 472 is missing expected H atoms. Skipping. Residue LYS 496 is missing expected H atoms. Skipping. Evaluate side-chains 11 residues out of total 109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 10 time to evaluate : 0.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 11 average time/residue: 0.2350 time to fit residues: 2.7756 Evaluate side-chains 11 residues out of total 109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 10 time to evaluate : 0.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 462 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 0.0470 chunk 6 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 8 optimal weight: 0.0980 chunk 0 optimal weight: 10.0000 chunk 7 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5157 r_free = 0.5157 target = 0.201605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.5015 r_free = 0.5015 target = 0.185735 restraints weight = 12952.280| |-----------------------------------------------------------------------------| r_work (start): 0.5008 rms_B_bonded: 9.61 r_work (final): 0.5008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0242 moved from start: 0.4717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 1007 Z= 0.099 Angle : 0.506 4.225 1366 Z= 0.263 Chirality : 0.030 0.093 165 Planarity : 0.002 0.023 176 Dihedral : 4.417 12.264 139 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.00 % Allowed : 15.15 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.36 (0.69), residues: 129 helix: -1.73 (0.52), residues: 89 sheet: None (None), residues: 0 loop : -3.10 (0.92), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 439 PHE 0.002 0.001 PHE A 480 TRP 0.002 0.000 TRP A 422 HIS 0.002 0.001 HIS A 457 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 1007) covalent geometry : angle 0.50588 ( 1366) hydrogen bonds : bond 0.02920 ( 40) hydrogen bonds : angle 3.82947 ( 117) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 400 is missing expected H atoms. Skipping. Residue LEU 401 is missing expected H atoms. Skipping. Residue SER 472 is missing expected H atoms. Skipping. Residue LYS 496 is missing expected H atoms. Skipping. Evaluate side-chains 9 residues out of total 109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.055 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 9 average time/residue: 0.2013 time to fit residues: 1.9842 Evaluate side-chains 9 residues out of total 109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 6 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 9 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 2 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 8 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 1 optimal weight: 0.4980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5019 r_free = 0.5019 target = 0.198928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4924 r_free = 0.4924 target = 0.176861 restraints weight = 8873.536| |-----------------------------------------------------------------------------| r_work (start): 0.4947 rms_B_bonded: 9.27 r_work (final): 0.4947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0091 moved from start: 0.5563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 1007 Z= 0.104 Angle : 0.508 3.963 1366 Z= 0.263 Chirality : 0.030 0.097 165 Planarity : 0.003 0.023 176 Dihedral : 4.221 13.169 139 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 1.01 % Allowed : 16.16 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.34 (0.76), residues: 129 helix: -1.00 (0.59), residues: 86 sheet: None (None), residues: 0 loop : -2.52 (0.97), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 491 PHE 0.003 0.001 PHE A 480 TRP 0.003 0.001 TRP A 474 HIS 0.003 0.001 HIS A 457 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 1007) covalent geometry : angle 0.50813 ( 1366) hydrogen bonds : bond 0.02362 ( 40) hydrogen bonds : angle 3.72616 ( 117) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 400 is missing expected H atoms. Skipping. Residue LEU 401 is missing expected H atoms. Skipping. Residue SER 472 is missing expected H atoms. Skipping. Residue LYS 496 is missing expected H atoms. Skipping. Evaluate side-chains 12 residues out of total 109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 11 time to evaluate : 0.057 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 12 average time/residue: 0.1740 time to fit residues: 2.2948 Evaluate side-chains 11 residues out of total 109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 10 time to evaluate : 0.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 462 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 4 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 11 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 1 optimal weight: 0.0370 chunk 10 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5181 r_free = 0.5181 target = 0.202914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.5050 r_free = 0.5050 target = 0.188958 restraints weight = 15492.503| |-----------------------------------------------------------------------------| r_work (start): 0.4919 rms_B_bonded: 9.48 r_work (final): 0.4919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0306 moved from start: 0.5826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 1007 Z= 0.092 Angle : 0.496 4.045 1366 Z= 0.252 Chirality : 0.030 0.094 165 Planarity : 0.002 0.023 176 Dihedral : 4.164 13.412 139 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.02 % Allowed : 15.15 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.95 (0.78), residues: 129 helix: -0.71 (0.60), residues: 86 sheet: None (None), residues: 0 loop : -2.33 (0.99), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 433 PHE 0.001 0.000 PHE A 480 TRP 0.001 0.000 TRP A 474 HIS 0.003 0.001 HIS A 457 Details of bonding type rmsd covalent geometry : bond 0.00215 ( 1007) covalent geometry : angle 0.49625 ( 1366) hydrogen bonds : bond 0.02364 ( 40) hydrogen bonds : angle 3.61403 ( 117) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 400 is missing expected H atoms. Skipping. Residue LEU 401 is missing expected H atoms. Skipping. Residue SER 472 is missing expected H atoms. Skipping. Residue LYS 496 is missing expected H atoms. Skipping. Evaluate side-chains 12 residues out of total 109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 10 time to evaluate : 0.053 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 12 average time/residue: 0.1752 time to fit residues: 2.2901 Evaluate side-chains 12 residues out of total 109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 11 time to evaluate : 0.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 462 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 8 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 12 optimal weight: 0.0030 chunk 1 optimal weight: 0.2980 chunk 9 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 2 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 overall best weight: 0.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5140 r_free = 0.5140 target = 0.201808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.5010 r_free = 0.5010 target = 0.187366 restraints weight = 14726.792| |-----------------------------------------------------------------------------| r_work (start): 0.4902 rms_B_bonded: 9.36 r_work (final): 0.4902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0283 moved from start: 0.6310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 1007 Z= 0.085 Angle : 0.487 3.943 1366 Z= 0.250 Chirality : 0.030 0.094 165 Planarity : 0.003 0.024 176 Dihedral : 3.949 13.036 139 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.01 % Allowed : 17.17 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.54 (0.80), residues: 129 helix: -0.40 (0.62), residues: 86 sheet: None (None), residues: 0 loop : -2.16 (1.03), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 491 PHE 0.002 0.001 PHE A 480 TRP 0.002 0.001 TRP A 436 HIS 0.003 0.001 HIS A 457 Details of bonding type rmsd covalent geometry : bond 0.00197 ( 1007) covalent geometry : angle 0.48732 ( 1366) hydrogen bonds : bond 0.02211 ( 40) hydrogen bonds : angle 3.39750 ( 117) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 400 is missing expected H atoms. Skipping. Residue LEU 401 is missing expected H atoms. Skipping. Residue SER 472 is missing expected H atoms. Skipping. Residue LYS 496 is missing expected H atoms. Skipping. Evaluate side-chains 11 residues out of total 109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 10 time to evaluate : 0.057 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 11 average time/residue: 0.1692 time to fit residues: 2.0270 Evaluate side-chains 10 residues out of total 109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 7 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 12 optimal weight: 0.0470 chunk 5 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 overall best weight: 1.0682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5020 r_free = 0.5020 target = 0.188149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4842 r_free = 0.4842 target = 0.166169 restraints weight = 12063.156| |-----------------------------------------------------------------------------| r_work (start): 0.4876 rms_B_bonded: 10.42 r_work (final): 0.4876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0394 moved from start: 0.7367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 1007 Z= 0.133 Angle : 0.586 4.804 1366 Z= 0.296 Chirality : 0.032 0.094 165 Planarity : 0.003 0.018 176 Dihedral : 4.387 16.004 139 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 1.01 % Allowed : 16.16 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.98 (0.76), residues: 129 helix: -0.72 (0.60), residues: 86 sheet: None (None), residues: 0 loop : -2.38 (0.94), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 465 PHE 0.003 0.001 PHE A 480 TRP 0.004 0.001 TRP A 474 HIS 0.003 0.002 HIS A 457 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 1007) covalent geometry : angle 0.58589 ( 1366) hydrogen bonds : bond 0.02362 ( 40) hydrogen bonds : angle 3.71041 ( 117) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 400 is missing expected H atoms. Skipping. Residue LEU 401 is missing expected H atoms. Skipping. Residue SER 472 is missing expected H atoms. Skipping. Residue LYS 496 is missing expected H atoms. Skipping. Evaluate side-chains 13 residues out of total 109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 12 time to evaluate : 0.052 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 508 MSE cc_start: 0.1565 (tpp) cc_final: 0.0989 (mmt) outliers start: 1 outliers final: 1 residues processed: 13 average time/residue: 0.2262 time to fit residues: 3.1377 Evaluate side-chains 11 residues out of total 109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 10 time to evaluate : 0.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 462 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 8 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5068 r_free = 0.5068 target = 0.187366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4848 r_free = 0.4848 target = 0.159488 restraints weight = 8703.581| |-----------------------------------------------------------------------------| r_work (start): 0.4851 rms_B_bonded: 9.68 r_work (final): 0.4851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0276 moved from start: 0.8113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 1007 Z= 0.101 Angle : 0.511 4.166 1366 Z= 0.264 Chirality : 0.030 0.094 165 Planarity : 0.003 0.017 176 Dihedral : 4.254 15.627 139 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.00 % Allowed : 18.18 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.36 (0.79), residues: 129 helix: -0.22 (0.61), residues: 83 sheet: None (None), residues: 0 loop : -2.06 (1.00), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 486 PHE 0.001 0.001 PHE A 480 TRP 0.003 0.001 TRP A 474 HIS 0.003 0.001 HIS A 457 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 1007) covalent geometry : angle 0.51138 ( 1366) hydrogen bonds : bond 0.02291 ( 40) hydrogen bonds : angle 3.54720 ( 117) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 400 is missing expected H atoms. Skipping. Residue LEU 401 is missing expected H atoms. Skipping. Residue SER 472 is missing expected H atoms. Skipping. Residue LYS 496 is missing expected H atoms. Skipping. Evaluate side-chains 9 residues out of total 109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.033 Fit side-chains revert: symmetry clash REVERT: A 508 MSE cc_start: 0.1966 (tpp) cc_final: 0.1464 (mmt) outliers start: 0 outliers final: 0 residues processed: 9 average time/residue: 0.1802 time to fit residues: 1.7444 Evaluate side-chains 9 residues out of total 109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 0 optimal weight: 9.9990 chunk 1 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 10 optimal weight: 0.0270 chunk 4 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 3 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 12 optimal weight: 0.0170 chunk 7 optimal weight: 0.4980 overall best weight: 0.3476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5073 r_free = 0.5073 target = 0.201779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4908 r_free = 0.4908 target = 0.178891 restraints weight = 9562.641| |-----------------------------------------------------------------------------| r_work (start): 0.4924 rms_B_bonded: 9.01 r_work (final): 0.4924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0274 moved from start: 0.8204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 1007 Z= 0.084 Angle : 0.488 4.536 1366 Z= 0.250 Chirality : 0.030 0.095 165 Planarity : 0.002 0.019 176 Dihedral : 3.965 14.660 139 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.00 % Allowed : 18.18 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.81), residues: 129 helix: 0.24 (0.63), residues: 83 sheet: None (None), residues: 0 loop : -2.00 (0.99), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 522 PHE 0.001 0.000 PHE A 480 TRP 0.002 0.000 TRP A 474 HIS 0.003 0.001 HIS A 457 Details of bonding type rmsd covalent geometry : bond 0.00192 ( 1007) covalent geometry : angle 0.48803 ( 1366) hydrogen bonds : bond 0.02120 ( 40) hydrogen bonds : angle 3.27443 ( 117) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 400 is missing expected H atoms. Skipping. Residue LEU 401 is missing expected H atoms. Skipping. Residue SER 472 is missing expected H atoms. Skipping. Residue LYS 496 is missing expected H atoms. Skipping. Evaluate side-chains 9 residues out of total 109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.039 Fit side-chains revert: symmetry clash REVERT: A 508 MSE cc_start: 0.1995 (tpp) cc_final: 0.1462 (mmt) outliers start: 0 outliers final: 0 residues processed: 9 average time/residue: 0.1868 time to fit residues: 1.8235 Evaluate side-chains 9 residues out of total 109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 4 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 5 optimal weight: 0.0370 chunk 8 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 2 optimal weight: 0.4980 chunk 7 optimal weight: 0.3980 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5114 r_free = 0.5114 target = 0.205665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4959 r_free = 0.4959 target = 0.189201 restraints weight = 15544.150| |-----------------------------------------------------------------------------| r_work (start): 0.4923 rms_B_bonded: 10.46 r_work (final): 0.4923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0363 moved from start: 0.8444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 1007 Z= 0.088 Angle : 0.500 5.336 1366 Z= 0.253 Chirality : 0.030 0.095 165 Planarity : 0.002 0.016 176 Dihedral : 3.884 14.323 139 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 0.00 % Allowed : 18.18 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.80), residues: 129 helix: 0.37 (0.61), residues: 82 sheet: None (None), residues: 0 loop : -1.75 (1.03), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 444 PHE 0.001 0.000 PHE A 480 TRP 0.002 0.001 TRP A 474 HIS 0.003 0.001 HIS A 457 Details of bonding type rmsd covalent geometry : bond 0.00201 ( 1007) covalent geometry : angle 0.49961 ( 1366) hydrogen bonds : bond 0.02164 ( 40) hydrogen bonds : angle 3.19632 ( 117) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1332.10 seconds wall clock time: 24 minutes 33.90 seconds (1473.90 seconds total)