Starting phenix.real_space_refine on Fri May 9 13:53:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xiz_33213/05_2025/7xiz_33213.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xiz_33213/05_2025/7xiz_33213.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xiz_33213/05_2025/7xiz_33213.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xiz_33213/05_2025/7xiz_33213.map" model { file = "/net/cci-nas-00/data/ceres_data/7xiz_33213/05_2025/7xiz_33213.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xiz_33213/05_2025/7xiz_33213.cif" } resolution = 3.74 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= 0.003 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 9 5.16 5 C 1386 2.51 5 N 364 2.21 5 O 402 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 2161 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 2133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2133 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 16, 'TRANS': 250} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.84, per 1000 atoms: 1.31 Number of scatterers: 2161 At special positions: 0 Unit cell: (76.96, 69.68, 76.96, 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 9 16.00 O 402 8.00 N 364 7.00 C 1386 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG B 601 " - " ASN B 331 " " NAG B 602 " - " ASN B 343 " Time building additional restraints: 0.50 Conformation dependent library (CDL) restraints added in 263.9 milliseconds 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 500 Finding SS restraints... Secondary structure from input PDB file: 2 helices and 3 sheets defined 4.5% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 386 through 390 removed outlier: 3.842A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.358A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP B 398 " --> pdb=" O VAL B 512 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 538 through 539 removed outlier: 4.825A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 542 through 543 34 hydrogen bonds defined for protein. 87 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: 0.45 Time building geometry restraints manager: 0.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 1 1.13 - 1.30: 345 1.30 - 1.48: 946 1.48 - 1.65: 918 1.65 - 1.82: 9 Bond restraints: 2219 Sorted by residual: bond pdb=" CG PRO B 384 " pdb=" CD PRO B 384 " ideal model delta sigma weight residual 1.503 0.960 0.543 3.40e-02 8.65e+02 2.56e+02 bond pdb=" N PRO B 384 " pdb=" CD PRO B 384 " ideal model delta sigma weight residual 1.473 1.574 -0.101 1.40e-02 5.10e+03 5.22e+01 bond pdb=" C1 NAG B 601 " pdb=" O5 NAG B 601 " ideal model delta sigma weight residual 1.406 1.494 -0.088 2.00e-02 2.50e+03 1.94e+01 bond pdb=" N PRO B 384 " pdb=" CA PRO B 384 " ideal model delta sigma weight residual 1.472 1.439 0.032 1.34e-02 5.57e+03 5.79e+00 bond pdb=" CB PRO B 384 " pdb=" CG PRO B 384 " ideal model delta sigma weight residual 1.492 1.600 -0.108 5.00e-02 4.00e+02 4.65e+00 ... (remaining 2214 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.93: 3002 4.93 - 9.86: 12 9.86 - 14.79: 1 14.79 - 19.72: 2 19.72 - 24.65: 1 Bond angle restraints: 3018 Sorted by residual: angle pdb=" N PRO B 384 " pdb=" CD PRO B 384 " pdb=" CG PRO B 384 " ideal model delta sigma weight residual 103.20 78.55 24.65 1.50e+00 4.44e-01 2.70e+02 angle pdb=" CA PRO B 384 " pdb=" N PRO B 384 " pdb=" CD PRO B 384 " ideal model delta sigma weight residual 112.00 96.26 15.74 1.40e+00 5.10e-01 1.26e+02 angle pdb=" CA PRO B 384 " pdb=" CB PRO B 384 " pdb=" CG PRO B 384 " ideal model delta sigma weight residual 104.50 87.29 17.21 1.90e+00 2.77e-01 8.20e+01 angle pdb=" N PRO B 384 " pdb=" CA PRO B 384 " pdb=" CB PRO B 384 " ideal model delta sigma weight residual 103.26 97.25 6.01 1.14e+00 7.69e-01 2.78e+01 angle pdb=" C PHE B 377 " pdb=" N LYS B 378 " pdb=" CA LYS B 378 " ideal model delta sigma weight residual 121.54 129.63 -8.09 1.91e+00 2.74e-01 1.79e+01 ... (remaining 3013 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.85: 1170 21.85 - 43.69: 142 43.69 - 65.53: 17 65.53 - 87.37: 8 87.37 - 109.21: 4 Dihedral angle restraints: 1341 sinusoidal: 560 harmonic: 781 Sorted by residual: dihedral pdb=" CA PHE B 377 " pdb=" C PHE B 377 " pdb=" N LYS B 378 " pdb=" CA LYS B 378 " ideal model delta harmonic sigma weight residual 180.00 151.18 28.82 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA ILE B 402 " pdb=" C ILE B 402 " pdb=" N ARG B 403 " pdb=" CA ARG B 403 " ideal model delta harmonic sigma weight residual -180.00 -161.02 -18.98 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA GLY B 476 " pdb=" C GLY B 476 " pdb=" N ASN B 477 " pdb=" CA ASN B 477 " ideal model delta harmonic sigma weight residual 180.00 161.17 18.83 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 1338 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 191 0.039 - 0.078: 83 0.078 - 0.117: 42 0.117 - 0.155: 7 0.155 - 0.194: 8 Chirality restraints: 331 Sorted by residual: chirality pdb=" CB VAL B 367 " pdb=" CA VAL B 367 " pdb=" CG1 VAL B 367 " pdb=" CG2 VAL B 367 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.19 2.00e-01 2.50e+01 9.44e-01 chirality pdb=" CA PHE B 377 " pdb=" N PHE B 377 " pdb=" C PHE B 377 " pdb=" CB PHE B 377 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.35e-01 chirality pdb=" C1 NAG B 601 " pdb=" ND2 ASN B 331 " pdb=" C2 NAG B 601 " pdb=" O5 NAG B 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 8.12e-01 ... (remaining 328 not shown) Planarity restraints: 395 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 383 " -0.097 5.00e-02 4.00e+02 1.34e-01 2.85e+01 pdb=" N PRO B 384 " 0.230 5.00e-02 4.00e+02 pdb=" CA PRO B 384 " -0.066 5.00e-02 4.00e+02 pdb=" CD PRO B 384 " -0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 378 " -0.014 2.00e-02 2.50e+03 2.87e-02 8.23e+00 pdb=" C LYS B 378 " 0.050 2.00e-02 2.50e+03 pdb=" O LYS B 378 " -0.019 2.00e-02 2.50e+03 pdb=" N CYS B 379 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 520 " 0.044 5.00e-02 4.00e+02 6.72e-02 7.23e+00 pdb=" N PRO B 521 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO B 521 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 521 " 0.037 5.00e-02 4.00e+02 ... (remaining 392 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 870 2.89 - 3.39: 1887 3.39 - 3.89: 3534 3.89 - 4.40: 3861 4.40 - 4.90: 6428 Nonbonded interactions: 16580 Sorted by model distance: nonbonded pdb=" N ASP B 571 " pdb=" OD1 ASP B 571 " model vdw 2.386 3.120 nonbonded pdb=" O GLN B 563 " pdb=" NH1 ARG B 577 " model vdw 2.395 3.120 nonbonded pdb=" NE2 GLN B 474 " pdb=" O ASN B 477 " model vdw 2.409 3.120 nonbonded pdb=" NE ARG B 457 " pdb=" O SER B 459 " model vdw 2.426 3.120 nonbonded pdb=" OG1 THR B 415 " pdb=" OD2 ASP B 420 " model vdw 2.440 3.040 ... (remaining 16575 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.390 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.130 Find NCS groups from input model: 0.020 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 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 : 0.013 0.543 2224 Z= 0.438 Angle : 1.114 24.653 3030 Z= 0.634 Chirality : 0.058 0.194 331 Planarity : 0.010 0.134 393 Dihedral : 19.025 109.212 832 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.75 % Allowed : 12.83 % Favored : 86.42 % Rotamer: Outliers : 0.00 % Allowed : 35.32 % Favored : 64.68 % 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: -3.37 (0.47), residues: 265 helix: -4.15 (0.66), residues: 19 sheet: -1.02 (0.70), residues: 48 loop : -2.57 (0.41), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 436 HIS 0.001 0.000 HIS B 505 PHE 0.019 0.002 PHE B 377 TYR 0.007 0.001 TYR B 451 ARG 0.001 0.000 ARG B 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00847 ( 2) link_NAG-ASN : angle 2.17568 ( 6) hydrogen bonds : bond 0.33402 ( 34) hydrogen bonds : angle 11.41332 ( 87) SS BOND : bond 0.00318 ( 3) SS BOND : angle 1.08932 ( 6) covalent geometry : bond 0.01271 ( 2219) covalent geometry : angle 1.11134 ( 3018) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.227 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.1152 time to fit residues: 3.1430 Evaluate side-chains 15 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 21 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 6 optimal weight: 7.9990 chunk 13 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 12 optimal weight: 8.9990 chunk 15 optimal weight: 0.0980 chunk 23 optimal weight: 7.9990 chunk 16 optimal weight: 20.0000 overall best weight: 3.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 540 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.077260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.066418 restraints weight = 10057.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.067715 restraints weight = 5913.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.068621 restraints weight = 4105.014| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 2224 Z= 0.186 Angle : 0.732 6.804 3030 Z= 0.377 Chirality : 0.050 0.163 331 Planarity : 0.007 0.057 393 Dihedral : 13.153 97.019 337 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.75 % Allowed : 15.85 % Favored : 83.40 % Rotamer: Outliers : 4.26 % Allowed : 35.32 % Favored : 60.43 % 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: -3.63 (0.46), residues: 265 helix: -4.22 (0.51), residues: 32 sheet: -1.30 (0.73), residues: 44 loop : -2.54 (0.43), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP B 353 HIS 0.001 0.000 HIS B 505 PHE 0.011 0.002 PHE B 456 TYR 0.007 0.002 TYR B 423 ARG 0.004 0.001 ARG B 577 Details of bonding type rmsd link_NAG-ASN : bond 0.00493 ( 2) link_NAG-ASN : angle 1.92032 ( 6) hydrogen bonds : bond 0.04721 ( 34) hydrogen bonds : angle 8.07880 ( 87) SS BOND : bond 0.00305 ( 3) SS BOND : angle 0.86022 ( 6) covalent geometry : bond 0.00424 ( 2219) covalent geometry : angle 0.72733 ( 3018) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 19 time to evaluate : 0.241 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 29 average time/residue: 0.0688 time to fit residues: 2.8602 Evaluate side-chains 22 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 15 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 17 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 4 optimal weight: 5.9990 chunk 1 optimal weight: 8.9990 chunk 13 optimal weight: 0.9980 chunk 25 optimal weight: 10.0000 chunk 10 optimal weight: 0.0020 chunk 7 optimal weight: 0.6980 overall best weight: 0.6588 ------------------------------------------------------------------------------- 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 = 0.3653 r_free = 0.3653 target = 0.079584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.069137 restraints weight = 9678.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.070482 restraints weight = 5650.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.071421 restraints weight = 3871.812| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 2224 Z= 0.110 Angle : 0.658 5.919 3030 Z= 0.331 Chirality : 0.047 0.157 331 Planarity : 0.006 0.056 393 Dihedral : 11.985 88.647 337 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.75 % Allowed : 13.21 % Favored : 86.04 % Rotamer: Outliers : 2.55 % Allowed : 36.60 % Favored : 60.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.22 (0.47), residues: 265 helix: -4.76 (0.52), residues: 18 sheet: -0.86 (0.75), residues: 42 loop : -2.38 (0.41), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 436 HIS 0.001 0.000 HIS B 519 PHE 0.007 0.001 PHE B 456 TYR 0.009 0.001 TYR B 421 ARG 0.003 0.000 ARG B 577 Details of bonding type rmsd link_NAG-ASN : bond 0.00553 ( 2) link_NAG-ASN : angle 2.33286 ( 6) hydrogen bonds : bond 0.03765 ( 34) hydrogen bonds : angle 7.02334 ( 87) SS BOND : bond 0.00270 ( 3) SS BOND : angle 0.66338 ( 6) covalent geometry : bond 0.00235 ( 2219) covalent geometry : angle 0.65062 ( 3018) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 17 time to evaluate : 0.255 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 23 average time/residue: 0.0777 time to fit residues: 2.5789 Evaluate side-chains 19 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 14 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 588 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 2 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 0 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 21 optimal weight: 0.7980 chunk 16 optimal weight: 7.9990 overall best weight: 3.4986 ------------------------------------------------------------------------------- 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 = 0.3577 r_free = 0.3577 target = 0.075380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.064946 restraints weight = 10138.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.066226 restraints weight = 6110.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.067126 restraints weight = 4261.300| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2224 Z= 0.200 Angle : 0.726 7.720 3030 Z= 0.371 Chirality : 0.051 0.175 331 Planarity : 0.007 0.056 393 Dihedral : 12.878 95.349 337 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.75 % Allowed : 16.60 % Favored : 82.64 % Rotamer: Outliers : 6.38 % Allowed : 34.04 % Favored : 59.57 % 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: -3.43 (0.47), residues: 265 helix: -4.52 (0.53), residues: 26 sheet: -1.13 (0.79), residues: 43 loop : -2.41 (0.42), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 353 HIS 0.000 0.000 HIS B 519 PHE 0.011 0.002 PHE B 456 TYR 0.007 0.002 TYR B 501 ARG 0.002 0.001 ARG B 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00486 ( 2) link_NAG-ASN : angle 1.73459 ( 6) hydrogen bonds : bond 0.04518 ( 34) hydrogen bonds : angle 7.62775 ( 87) SS BOND : bond 0.00222 ( 3) SS BOND : angle 0.72913 ( 6) covalent geometry : bond 0.00434 ( 2219) covalent geometry : angle 0.72283 ( 3018) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 19 time to evaluate : 0.252 Fit side-chains revert: symmetry clash REVERT: B 324 GLU cc_start: 0.7071 (OUTLIER) cc_final: 0.6532 (mm-30) REVERT: B 347 PHE cc_start: 0.5754 (OUTLIER) cc_final: 0.5333 (m-10) outliers start: 15 outliers final: 12 residues processed: 33 average time/residue: 0.1047 time to fit residues: 4.4361 Evaluate side-chains 29 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 15 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 588 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 25 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 20 optimal weight: 10.0000 chunk 10 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 13 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 chunk 4 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3624 r_free = 0.3624 target = 0.077708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.066949 restraints weight = 9953.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.068297 restraints weight = 5905.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.069258 restraints weight = 4124.338| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 2224 Z= 0.122 Angle : 0.707 7.688 3030 Z= 0.354 Chirality : 0.049 0.170 331 Planarity : 0.006 0.056 393 Dihedral : 12.123 89.708 337 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.75 % Allowed : 13.58 % Favored : 85.66 % Rotamer: Outliers : 7.23 % Allowed : 33.19 % Favored : 59.57 % 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: -3.36 (0.46), residues: 265 helix: -4.93 (0.44), residues: 18 sheet: -1.15 (0.85), residues: 33 loop : -2.39 (0.40), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 436 HIS 0.001 0.000 HIS B 505 PHE 0.007 0.001 PHE B 429 TYR 0.009 0.001 TYR B 421 ARG 0.002 0.000 ARG B 577 Details of bonding type rmsd link_NAG-ASN : bond 0.00470 ( 2) link_NAG-ASN : angle 2.26225 ( 6) hydrogen bonds : bond 0.03248 ( 34) hydrogen bonds : angle 7.03395 ( 87) SS BOND : bond 0.01586 ( 3) SS BOND : angle 3.29622 ( 6) covalent geometry : bond 0.00279 ( 2219) covalent geometry : angle 0.68579 ( 3018) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 19 time to evaluate : 0.230 Fit side-chains outliers start: 17 outliers final: 11 residues processed: 35 average time/residue: 0.0927 time to fit residues: 4.2095 Evaluate side-chains 28 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 17 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 588 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 25 optimal weight: 6.9990 chunk 8 optimal weight: 0.0980 chunk 6 optimal weight: 4.9990 chunk 12 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 2 optimal weight: 7.9990 chunk 18 optimal weight: 0.3980 chunk 4 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- 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 = 0.3585 r_free = 0.3585 target = 0.075456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.064563 restraints weight = 10058.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.065849 restraints weight = 6120.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.066807 restraints weight = 4356.610| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 2224 Z= 0.169 Angle : 0.749 10.154 3030 Z= 0.379 Chirality : 0.051 0.168 331 Planarity : 0.006 0.055 393 Dihedral : 12.453 91.972 337 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.75 % Allowed : 16.98 % Favored : 82.26 % Rotamer: Outliers : 6.81 % Allowed : 30.21 % Favored : 62.98 % 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: -3.29 (0.49), residues: 265 helix: -4.49 (0.60), residues: 25 sheet: -1.28 (0.78), residues: 43 loop : -2.25 (0.43), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP B 353 HIS 0.000 0.000 HIS B 505 PHE 0.009 0.001 PHE B 497 TYR 0.007 0.001 TYR B 501 ARG 0.003 0.000 ARG B 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00398 ( 2) link_NAG-ASN : angle 1.92388 ( 6) hydrogen bonds : bond 0.03587 ( 34) hydrogen bonds : angle 7.30552 ( 87) SS BOND : bond 0.01922 ( 3) SS BOND : angle 4.41151 ( 6) covalent geometry : bond 0.00385 ( 2219) covalent geometry : angle 0.71885 ( 3018) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 19 time to evaluate : 0.252 Fit side-chains REVERT: B 347 PHE cc_start: 0.5635 (OUTLIER) cc_final: 0.5264 (m-10) outliers start: 16 outliers final: 13 residues processed: 34 average time/residue: 0.0702 time to fit residues: 3.4093 Evaluate side-chains 31 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 17 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 588 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 24 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 8.9990 chunk 5 optimal weight: 1.9990 chunk 12 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 chunk 13 optimal weight: 0.1980 chunk 14 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 4 optimal weight: 7.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- 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 = 0.3617 r_free = 0.3617 target = 0.076847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.065907 restraints weight = 10023.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.067278 restraints weight = 6056.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.068152 restraints weight = 4234.257| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 2224 Z= 0.133 Angle : 0.725 8.402 3030 Z= 0.363 Chirality : 0.050 0.163 331 Planarity : 0.006 0.055 393 Dihedral : 12.177 90.031 337 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.75 % Allowed : 15.85 % Favored : 83.40 % Rotamer: Outliers : 6.38 % Allowed : 30.21 % Favored : 63.40 % 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: -3.54 (0.47), residues: 265 helix: -4.52 (0.54), residues: 31 sheet: -1.19 (0.80), residues: 41 loop : -2.42 (0.43), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 436 HIS 0.000 0.000 HIS B 505 PHE 0.008 0.001 PHE B 497 TYR 0.006 0.001 TYR B 501 ARG 0.002 0.000 ARG B 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00440 ( 2) link_NAG-ASN : angle 2.09442 ( 6) hydrogen bonds : bond 0.03211 ( 34) hydrogen bonds : angle 7.03672 ( 87) SS BOND : bond 0.01552 ( 3) SS BOND : angle 3.76700 ( 6) covalent geometry : bond 0.00303 ( 2219) covalent geometry : angle 0.70064 ( 3018) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 19 time to evaluate : 0.246 Fit side-chains REVERT: B 347 PHE cc_start: 0.5627 (OUTLIER) cc_final: 0.5317 (m-10) outliers start: 15 outliers final: 14 residues processed: 33 average time/residue: 0.0678 time to fit residues: 3.2523 Evaluate side-chains 31 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 16 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 588 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 5 optimal weight: 8.9990 chunk 11 optimal weight: 6.9990 chunk 6 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 13 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 19 optimal weight: 0.0870 chunk 4 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 overall best weight: 1.1562 ------------------------------------------------------------------------------- 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 = 0.3634 r_free = 0.3634 target = 0.077703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.066771 restraints weight = 10252.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.068170 restraints weight = 6129.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.069136 restraints weight = 4276.253| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 2224 Z= 0.121 Angle : 0.725 8.006 3030 Z= 0.360 Chirality : 0.050 0.167 331 Planarity : 0.006 0.057 393 Dihedral : 11.980 87.752 337 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.75 % Allowed : 14.72 % Favored : 84.53 % Rotamer: Outliers : 6.38 % Allowed : 29.79 % Favored : 63.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.48 (0.47), residues: 265 helix: -4.95 (0.33), residues: 24 sheet: -1.30 (0.76), residues: 43 loop : -2.38 (0.42), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 436 HIS 0.001 0.000 HIS B 505 PHE 0.008 0.001 PHE B 497 TYR 0.007 0.001 TYR B 421 ARG 0.002 0.000 ARG B 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00420 ( 2) link_NAG-ASN : angle 2.19620 ( 6) hydrogen bonds : bond 0.03182 ( 34) hydrogen bonds : angle 6.76330 ( 87) SS BOND : bond 0.01387 ( 3) SS BOND : angle 3.36126 ( 6) covalent geometry : bond 0.00275 ( 2219) covalent geometry : angle 0.70372 ( 3018) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 17 time to evaluate : 0.247 Fit side-chains REVERT: B 365 TYR cc_start: 0.7442 (m-80) cc_final: 0.6992 (m-80) outliers start: 15 outliers final: 14 residues processed: 31 average time/residue: 0.0649 time to fit residues: 2.9848 Evaluate side-chains 31 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 17 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 588 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 62.8944 > 50: distance: 78 - 82: 20.061 distance: 82 - 83: 44.968 distance: 83 - 84: 54.415 distance: 83 - 86: 18.066 distance: 84 - 85: 44.162 distance: 84 - 90: 23.085 distance: 86 - 87: 36.654 distance: 87 - 88: 32.957 distance: 87 - 89: 18.913 distance: 90 - 91: 38.548 distance: 91 - 92: 27.707 distance: 91 - 94: 46.778 distance: 92 - 93: 25.274 distance: 92 - 102: 36.773 distance: 94 - 95: 13.934 distance: 95 - 96: 40.539 distance: 95 - 97: 44.804 distance: 96 - 98: 15.709 distance: 97 - 99: 15.376 distance: 98 - 100: 9.048 distance: 99 - 100: 7.514 distance: 102 - 103: 44.658 distance: 103 - 104: 39.470 distance: 103 - 106: 12.562 distance: 104 - 105: 41.947 distance: 104 - 111: 23.229 distance: 106 - 107: 22.066 distance: 107 - 108: 38.580 distance: 108 - 109: 26.150 distance: 109 - 110: 48.934 distance: 111 - 112: 32.674 distance: 112 - 113: 39.807 distance: 112 - 115: 38.903 distance: 113 - 114: 25.682 distance: 113 - 119: 17.936 distance: 115 - 116: 61.048 distance: 116 - 117: 31.808 distance: 116 - 118: 44.348 distance: 119 - 120: 35.653 distance: 119 - 125: 52.673 distance: 120 - 121: 12.500 distance: 120 - 123: 8.700 distance: 121 - 122: 42.644 distance: 121 - 126: 33.459 distance: 123 - 124: 25.072 distance: 124 - 125: 37.069 distance: 126 - 127: 31.370 distance: 127 - 128: 18.635 distance: 127 - 130: 13.741 distance: 128 - 129: 33.338 distance: 128 - 134: 18.093 distance: 130 - 131: 6.100 distance: 131 - 132: 26.170 distance: 131 - 133: 17.208 distance: 134 - 135: 22.413 distance: 135 - 136: 5.341 distance: 135 - 138: 31.524 distance: 136 - 137: 27.876 distance: 136 - 142: 29.098 distance: 138 - 139: 18.243 distance: 139 - 140: 40.535 distance: 139 - 141: 17.000 distance: 142 - 143: 27.319 distance: 143 - 144: 18.891 distance: 143 - 146: 23.730 distance: 144 - 145: 39.200 distance: 144 - 153: 27.928 distance: 146 - 147: 18.409 distance: 147 - 148: 20.478 distance: 147 - 149: 20.690 distance: 148 - 150: 14.987 distance: 149 - 151: 8.124 distance: 150 - 152: 21.219 distance: 151 - 152: 22.962 distance: 153 - 154: 30.590 distance: 154 - 155: 24.954 distance: 154 - 157: 27.965 distance: 155 - 156: 40.340 distance: 155 - 160: 20.820 distance: 157 - 158: 24.453 distance: 157 - 159: 30.302 distance: 160 - 161: 16.444 distance: 161 - 162: 46.483 distance: 162 - 163: 32.910 distance: 162 - 164: 30.523