Starting phenix.real_space_refine on Sat Apr 26 18:27:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n5g_24189/04_2025/7n5g_24189.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n5g_24189/04_2025/7n5g_24189.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7n5g_24189/04_2025/7n5g_24189.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n5g_24189/04_2025/7n5g_24189.map" model { file = "/net/cci-nas-00/data/ceres_data/7n5g_24189/04_2025/7n5g_24189.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n5g_24189/04_2025/7n5g_24189.cif" } resolution = 2.4 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= 0.001 sd= 0.023 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 12 5.16 5 C 1920 2.51 5 N 486 2.21 5 O 508 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 2926 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 2908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2908 Classifications: {'peptide': 371} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 7, 'TRANS': 363} Chain breaks: 4 Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 170 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 1, 'TRP:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 50 Chain: "B" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.86, per 1000 atoms: 0.98 Number of scatterers: 2926 At special positions: 0 Unit cell: (70.04, 93.73, 140.08, 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 12 16.00 O 508 8.00 N 486 7.00 C 1920 6.00 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: 0.89 Conformation dependent library (CDL) restraints added in 460.4 milliseconds 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 720 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 2 sheets defined 63.9% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'B' and resid 186 through 203 Processing helix chain 'B' and resid 223 through 232 Processing helix chain 'B' and resid 235 through 241 Processing helix chain 'B' and resid 265 through 285 Processing helix chain 'B' and resid 295 through 329 removed outlier: 3.824A pdb=" N LEU B 299 " --> pdb=" O THR B 295 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER B 329 " --> pdb=" O ILE B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 331 No H-bonds generated for 'chain 'B' and resid 330 through 331' Processing helix chain 'B' and resid 332 through 334 No H-bonds generated for 'chain 'B' and resid 332 through 334' Processing helix chain 'B' and resid 335 through 349 Processing helix chain 'B' and resid 508 through 524 Processing helix chain 'B' and resid 526 through 552 Processing helix chain 'B' and resid 556 through 590 removed outlier: 5.467A pdb=" N ASN B 576 " --> pdb=" O PHE B 572 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N THR B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 635 Processing helix chain 'B' and resid 661 through 678 Processing helix chain 'B' and resid 714 through 737 Processing sheet with id=AA1, first strand: chain 'B' and resid 626 through 630 removed outlier: 7.157A pdb=" N THR B 616 " --> pdb=" O MET B 612 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N MET B 612 " --> pdb=" O THR B 616 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL B 618 " --> pdb=" O GLU B 610 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 649 through 657 removed outlier: 6.485A pdb=" N LYS B 699 " --> pdb=" O ILE B 694 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ILE B 694 " --> pdb=" O LYS B 699 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LYS B 701 " --> pdb=" O LYS B 692 " (cutoff:3.500A) 206 hydrogen bonds defined for protein. 612 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: 0.79 Time building geometry restraints manager: 1.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 675 1.32 - 1.44: 718 1.44 - 1.57: 1550 1.57 - 1.69: 16 1.69 - 1.81: 21 Bond restraints: 2980 Sorted by residual: bond pdb=" CD2 TRP B 507 " pdb=" CE3 TRP B 507 " ideal model delta sigma weight residual 1.398 1.503 -0.105 1.60e-02 3.91e+03 4.27e+01 bond pdb=" CZ2 TRP B 507 " pdb=" CH2 TRP B 507 " ideal model delta sigma weight residual 1.368 1.480 -0.112 1.90e-02 2.77e+03 3.46e+01 bond pdb=" CB ILE B 285 " pdb=" CG1 ILE B 285 " ideal model delta sigma weight residual 1.530 1.635 -0.105 2.00e-02 2.50e+03 2.77e+01 bond pdb=" CB TYR B 629 " pdb=" CG TYR B 629 " ideal model delta sigma weight residual 1.512 1.399 0.113 2.20e-02 2.07e+03 2.65e+01 bond pdb=" CB HIS B 345 " pdb=" CG HIS B 345 " ideal model delta sigma weight residual 1.497 1.428 0.069 1.40e-02 5.10e+03 2.46e+01 ... (remaining 2975 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 3160 1.65 - 3.30: 695 3.30 - 4.95: 146 4.95 - 6.59: 33 6.59 - 8.24: 5 Bond angle restraints: 4039 Sorted by residual: angle pdb=" C HIS B 592 " pdb=" N PRO B 593 " pdb=" CA PRO B 593 " ideal model delta sigma weight residual 119.56 126.54 -6.98 1.01e+00 9.80e-01 4.78e+01 angle pdb=" C SER B 645 " pdb=" N PRO B 646 " pdb=" CA PRO B 646 " ideal model delta sigma weight residual 120.52 126.91 -6.39 9.90e-01 1.02e+00 4.17e+01 angle pdb=" C LEU B 743 " pdb=" N PRO B 744 " pdb=" CA PRO B 744 " ideal model delta sigma weight residual 119.85 126.24 -6.39 1.01e+00 9.80e-01 4.00e+01 angle pdb=" C GLN B 291 " pdb=" N PRO B 292 " pdb=" CA PRO B 292 " ideal model delta sigma weight residual 119.28 125.41 -6.13 1.10e+00 8.26e-01 3.11e+01 angle pdb=" N SER B 267 " pdb=" CA SER B 267 " pdb=" C SER B 267 " ideal model delta sigma weight residual 112.23 105.58 6.65 1.26e+00 6.30e-01 2.79e+01 ... (remaining 4034 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.33: 1685 14.33 - 28.65: 62 28.65 - 42.97: 7 42.97 - 57.30: 11 57.30 - 71.62: 6 Dihedral angle restraints: 1771 sinusoidal: 680 harmonic: 1091 Sorted by residual: dihedral pdb=" CA ASP B 657 " pdb=" CB ASP B 657 " pdb=" CG ASP B 657 " pdb=" OD1 ASP B 657 " ideal model delta sinusoidal sigma weight residual -30.00 -84.87 54.87 1 2.00e+01 2.50e-03 1.02e+01 dihedral pdb=" CA ASP B 595 " pdb=" CB ASP B 595 " pdb=" CG ASP B 595 " pdb=" OD1 ASP B 595 " ideal model delta sinusoidal sigma weight residual -30.00 -74.43 44.43 1 2.00e+01 2.50e-03 6.86e+00 dihedral pdb=" N ASP B 650 " pdb=" C ASP B 650 " pdb=" CA ASP B 650 " pdb=" CB ASP B 650 " ideal model delta harmonic sigma weight residual 122.80 116.39 6.41 0 2.50e+00 1.60e-01 6.57e+00 ... (remaining 1768 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 371 0.097 - 0.193: 99 0.193 - 0.290: 16 0.290 - 0.387: 3 0.387 - 0.483: 2 Chirality restraints: 491 Sorted by residual: chirality pdb=" CG LEU B 264 " pdb=" CB LEU B 264 " pdb=" CD1 LEU B 264 " pdb=" CD2 LEU B 264 " both_signs ideal model delta sigma weight residual False -2.59 -3.07 0.48 2.00e-01 2.50e+01 5.84e+00 chirality pdb=" CB ILE B 285 " pdb=" CA ILE B 285 " pdb=" CG1 ILE B 285 " pdb=" CG2 ILE B 285 " both_signs ideal model delta sigma weight residual False 2.64 3.05 -0.40 2.00e-01 2.50e+01 4.06e+00 chirality pdb=" CA TRP B 304 " pdb=" N TRP B 304 " pdb=" C TRP B 304 " pdb=" CB TRP B 304 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.19e+00 ... (remaining 488 not shown) Planarity restraints: 493 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 697 " 0.015 2.00e-02 2.50e+03 3.07e-02 9.41e+00 pdb=" C VAL B 697 " -0.053 2.00e-02 2.50e+03 pdb=" O VAL B 697 " 0.020 2.00e-02 2.50e+03 pdb=" N ASN B 698 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 675 " 0.035 2.00e-02 2.50e+03 1.98e-02 7.85e+00 pdb=" CG TYR B 675 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR B 675 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR B 675 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR B 675 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR B 675 " -0.013 2.00e-02 2.50e+03 pdb=" CZ TYR B 675 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR B 675 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 741 " -0.012 2.00e-02 2.50e+03 2.42e-02 5.86e+00 pdb=" C ASN B 741 " 0.042 2.00e-02 2.50e+03 pdb=" O ASN B 741 " -0.016 2.00e-02 2.50e+03 pdb=" N LEU B 742 " -0.014 2.00e-02 2.50e+03 ... (remaining 490 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 1125 2.89 - 3.39: 2994 3.39 - 3.89: 4759 3.89 - 4.40: 5429 4.40 - 4.90: 8451 Nonbonded interactions: 22758 Sorted by model distance: nonbonded pdb=" OD1 ASP B 737 " pdb=" NZ LYS B 739 " model vdw 2.386 3.120 nonbonded pdb=" N VAL B 697 " pdb=" N ASN B 698 " model vdw 2.467 2.560 nonbonded pdb=" N ASN B 711 " pdb=" O ASN B 711 " model vdw 2.498 2.496 nonbonded pdb=" N PRO B 646 " pdb=" O PRO B 646 " model vdw 2.533 2.496 nonbonded pdb=" N ASN B 613 " pdb=" O ASN B 613 " model vdw 2.553 2.496 ... (remaining 22753 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: 1.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.160 Find NCS groups from input model: 0.030 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:13.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 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 : 0.022 0.132 2980 Z= 1.192 Angle : 1.511 8.243 4039 Z= 1.034 Chirality : 0.093 0.483 491 Planarity : 0.008 0.031 493 Dihedral : 10.569 71.622 1051 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 0.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.41), residues: 361 helix: 1.41 (0.30), residues: 223 sheet: 0.94 (0.88), residues: 42 loop : 1.21 (0.65), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.008 TRP B 683 HIS 0.005 0.002 HIS B 346 PHE 0.019 0.005 PHE B 682 TYR 0.035 0.008 TYR B 675 ARG 0.005 0.001 ARG B 338 Details of bonding type rmsd hydrogen bonds : bond 0.14388 ( 206) hydrogen bonds : angle 5.83451 ( 612) covalent geometry : bond 0.02231 ( 2980) covalent geometry : angle 1.51055 ( 4039) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.326 Fit side-chains revert: symmetry clash REVERT: B 526 LYS cc_start: 0.7984 (mttt) cc_final: 0.7595 (mtpp) REVERT: B 624 LYS cc_start: 0.8434 (mmtm) cc_final: 0.7572 (tttp) REVERT: B 702 MET cc_start: 0.8860 (mtt) cc_final: 0.8638 (mtp) outliers start: 0 outliers final: 1 residues processed: 99 average time/residue: 1.1773 time to fit residues: 119.4227 Evaluate side-chains 85 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 84 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 560 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 31 optimal weight: 0.0050 chunk 28 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 11 optimal weight: 6.9990 chunk 17 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 531 GLN B 605 ASN B 648 GLN B 688 ASN B 698 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.160441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.133775 restraints weight = 4006.734| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 1.66 r_work: 0.3739 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3605 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2980 Z= 0.141 Angle : 0.488 6.378 4039 Z= 0.262 Chirality : 0.041 0.144 491 Planarity : 0.003 0.040 493 Dihedral : 8.461 54.634 397 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 4.56 % Allowed : 9.12 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.74 (0.43), residues: 361 helix: 2.50 (0.32), residues: 229 sheet: 0.48 (0.76), residues: 42 loop : 0.76 (0.68), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 281 HIS 0.002 0.001 HIS B 592 PHE 0.012 0.002 PHE B 271 TYR 0.005 0.001 TYR B 740 ARG 0.004 0.001 ARG B 720 Details of bonding type rmsd hydrogen bonds : bond 0.05293 ( 206) hydrogen bonds : angle 3.89492 ( 612) covalent geometry : bond 0.00293 ( 2980) covalent geometry : angle 0.48819 ( 4039) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: B 283 MET cc_start: 0.5755 (tpp) cc_final: 0.5447 (mmm) outliers start: 14 outliers final: 6 residues processed: 95 average time/residue: 1.1932 time to fit residues: 116.1518 Evaluate side-chains 91 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 543 MET Chi-restraints excluded: chain B residue 560 ILE Chi-restraints excluded: chain B residue 562 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 28 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 32 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 531 GLN B 688 ASN B 698 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.159291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.133386 restraints weight = 3951.886| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 1.55 r_work: 0.3736 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3604 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2980 Z= 0.143 Angle : 0.452 6.763 4039 Z= 0.241 Chirality : 0.040 0.135 491 Planarity : 0.003 0.029 493 Dihedral : 8.023 54.557 397 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 3.26 % Allowed : 12.38 % Favored : 84.36 % 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: 3.05 (0.43), residues: 361 helix: 2.83 (0.32), residues: 229 sheet: 0.59 (0.76), residues: 42 loop : 0.62 (0.68), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 548 HIS 0.004 0.001 HIS B 708 PHE 0.010 0.002 PHE B 654 TYR 0.008 0.001 TYR B 740 ARG 0.002 0.000 ARG B 720 Details of bonding type rmsd hydrogen bonds : bond 0.04895 ( 206) hydrogen bonds : angle 3.65759 ( 612) covalent geometry : bond 0.00318 ( 2980) covalent geometry : angle 0.45194 ( 4039) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.408 Fit side-chains revert: symmetry clash REVERT: B 624 LYS cc_start: 0.8731 (mmtm) cc_final: 0.7634 (tmmt) outliers start: 10 outliers final: 6 residues processed: 92 average time/residue: 1.1670 time to fit residues: 110.1259 Evaluate side-chains 89 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 543 MET Chi-restraints excluded: chain B residue 560 ILE Chi-restraints excluded: chain B residue 562 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 2 optimal weight: 2.9990 chunk 1 optimal weight: 9.9990 chunk 32 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 21 optimal weight: 0.1980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 525 ASN B 531 GLN B 648 GLN B 688 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.159977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.133044 restraints weight = 4083.261| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 1.67 r_work: 0.3726 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3591 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2980 Z= 0.128 Angle : 0.439 6.937 4039 Z= 0.229 Chirality : 0.039 0.137 491 Planarity : 0.002 0.029 493 Dihedral : 7.721 55.112 397 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 3.91 % Allowed : 14.01 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.22 (0.44), residues: 361 helix: 3.06 (0.32), residues: 229 sheet: 0.68 (0.79), residues: 42 loop : 0.39 (0.67), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 548 HIS 0.004 0.001 HIS B 708 PHE 0.011 0.001 PHE B 654 TYR 0.007 0.001 TYR B 740 ARG 0.001 0.000 ARG B 720 Details of bonding type rmsd hydrogen bonds : bond 0.04450 ( 206) hydrogen bonds : angle 3.50945 ( 612) covalent geometry : bond 0.00283 ( 2980) covalent geometry : angle 0.43894 ( 4039) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: B 624 LYS cc_start: 0.8781 (mmtm) cc_final: 0.7730 (tmmt) outliers start: 12 outliers final: 9 residues processed: 92 average time/residue: 1.2756 time to fit residues: 120.1750 Evaluate side-chains 93 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain B residue 525 ASN Chi-restraints excluded: chain B residue 543 MET Chi-restraints excluded: chain B residue 560 ILE Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 579 LYS Chi-restraints excluded: chain B residue 662 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 10 optimal weight: 0.0030 chunk 5 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 525 ASN B 531 GLN B 648 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.159601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.134787 restraints weight = 4007.072| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 1.79 r_work: 0.3719 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3583 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2980 Z= 0.135 Angle : 0.441 7.245 4039 Z= 0.229 Chirality : 0.040 0.146 491 Planarity : 0.002 0.029 493 Dihedral : 7.685 56.909 397 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 3.58 % Allowed : 14.66 % Favored : 81.76 % 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 (0.44), residues: 361 helix: 3.09 (0.32), residues: 229 sheet: 0.65 (0.78), residues: 42 loop : 0.27 (0.67), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 548 HIS 0.004 0.001 HIS B 708 PHE 0.010 0.001 PHE B 271 TYR 0.007 0.001 TYR B 740 ARG 0.001 0.000 ARG B 720 Details of bonding type rmsd hydrogen bonds : bond 0.04504 ( 206) hydrogen bonds : angle 3.49737 ( 612) covalent geometry : bond 0.00302 ( 2980) covalent geometry : angle 0.44106 ( 4039) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.340 Fit side-chains REVERT: B 525 ASN cc_start: 0.7085 (OUTLIER) cc_final: 0.6821 (t160) REVERT: B 624 LYS cc_start: 0.8802 (mmtm) cc_final: 0.7752 (tmmt) outliers start: 11 outliers final: 6 residues processed: 92 average time/residue: 1.2523 time to fit residues: 118.0478 Evaluate side-chains 93 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 525 ASN Chi-restraints excluded: chain B residue 560 ILE Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 579 LYS Chi-restraints excluded: chain B residue 662 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 1 optimal weight: 10.0000 chunk 12 optimal weight: 0.0020 chunk 14 optimal weight: 2.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 525 ASN B 531 GLN B 648 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.159895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.134916 restraints weight = 4111.092| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 1.84 r_work: 0.3726 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3588 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2980 Z= 0.124 Angle : 0.440 7.657 4039 Z= 0.227 Chirality : 0.040 0.155 491 Planarity : 0.002 0.029 493 Dihedral : 7.600 57.731 397 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 4.23 % Allowed : 13.68 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.28 (0.44), residues: 361 helix: 3.17 (0.32), residues: 229 sheet: 0.62 (0.79), residues: 42 loop : 0.22 (0.67), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 548 HIS 0.004 0.001 HIS B 708 PHE 0.010 0.001 PHE B 654 TYR 0.007 0.001 TYR B 740 ARG 0.002 0.000 ARG B 720 Details of bonding type rmsd hydrogen bonds : bond 0.04367 ( 206) hydrogen bonds : angle 3.47677 ( 612) covalent geometry : bond 0.00270 ( 2980) covalent geometry : angle 0.44042 ( 4039) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: B 525 ASN cc_start: 0.7119 (OUTLIER) cc_final: 0.6777 (t0) REVERT: B 624 LYS cc_start: 0.8790 (mmtm) cc_final: 0.7781 (tmmt) REVERT: B 737 ASP cc_start: 0.7789 (t0) cc_final: 0.7508 (t0) outliers start: 13 outliers final: 8 residues processed: 91 average time/residue: 1.2232 time to fit residues: 114.0398 Evaluate side-chains 96 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain B residue 525 ASN Chi-restraints excluded: chain B residue 543 MET Chi-restraints excluded: chain B residue 560 ILE Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 579 LYS Chi-restraints excluded: chain B residue 678 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 30 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 23 optimal weight: 0.2980 chunk 18 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 525 ASN B 531 GLN B 648 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.159774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.133025 restraints weight = 4054.184| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 1.66 r_work: 0.3724 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3589 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2980 Z= 0.132 Angle : 0.448 7.890 4039 Z= 0.229 Chirality : 0.040 0.158 491 Planarity : 0.002 0.028 493 Dihedral : 7.524 59.043 397 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 3.91 % Allowed : 14.01 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.26 (0.44), residues: 361 helix: 3.19 (0.32), residues: 229 sheet: 0.61 (0.80), residues: 42 loop : 0.15 (0.67), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 548 HIS 0.004 0.001 HIS B 708 PHE 0.011 0.001 PHE B 654 TYR 0.007 0.001 TYR B 740 ARG 0.002 0.000 ARG B 720 Details of bonding type rmsd hydrogen bonds : bond 0.04398 ( 206) hydrogen bonds : angle 3.48074 ( 612) covalent geometry : bond 0.00296 ( 2980) covalent geometry : angle 0.44757 ( 4039) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: B 525 ASN cc_start: 0.7142 (OUTLIER) cc_final: 0.6860 (t0) REVERT: B 624 LYS cc_start: 0.8806 (mmtm) cc_final: 0.7836 (tmmt) outliers start: 12 outliers final: 9 residues processed: 91 average time/residue: 1.2302 time to fit residues: 114.5849 Evaluate side-chains 97 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 525 ASN Chi-restraints excluded: chain B residue 543 MET Chi-restraints excluded: chain B residue 560 ILE Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 579 LYS Chi-restraints excluded: chain B residue 662 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 33 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 10 optimal weight: 0.0070 chunk 12 optimal weight: 10.0000 chunk 25 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 36 optimal weight: 0.0870 overall best weight: 0.5176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 525 ASN B 531 GLN B 648 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.160079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.135357 restraints weight = 4080.666| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 1.81 r_work: 0.3732 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3594 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2980 Z= 0.115 Angle : 0.438 8.407 4039 Z= 0.224 Chirality : 0.039 0.154 491 Planarity : 0.002 0.028 493 Dihedral : 7.454 59.345 397 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 4.56 % Allowed : 13.68 % Favored : 81.76 % 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: 3.31 (0.44), residues: 361 helix: 3.25 (0.32), residues: 229 sheet: 0.56 (0.80), residues: 42 loop : 0.13 (0.68), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 548 HIS 0.003 0.001 HIS B 708 PHE 0.012 0.001 PHE B 654 TYR 0.007 0.001 TYR B 740 ARG 0.001 0.000 ARG B 720 Details of bonding type rmsd hydrogen bonds : bond 0.04225 ( 206) hydrogen bonds : angle 3.44661 ( 612) covalent geometry : bond 0.00246 ( 2980) covalent geometry : angle 0.43808 ( 4039) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.364 Fit side-chains revert: symmetry clash REVERT: B 525 ASN cc_start: 0.7019 (OUTLIER) cc_final: 0.6736 (t0) REVERT: B 624 LYS cc_start: 0.8800 (mmtm) cc_final: 0.7782 (tmmt) outliers start: 14 outliers final: 11 residues processed: 92 average time/residue: 1.1908 time to fit residues: 112.2103 Evaluate side-chains 99 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 525 ASN Chi-restraints excluded: chain B residue 543 MET Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 560 ILE Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 579 LYS Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 678 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 28 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 3 optimal weight: 0.0870 chunk 21 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 20 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 525 ASN B 531 GLN B 648 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.159732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.132870 restraints weight = 4037.932| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 1.67 r_work: 0.3725 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3587 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2980 Z= 0.132 Angle : 0.451 9.055 4039 Z= 0.228 Chirality : 0.039 0.121 491 Planarity : 0.002 0.028 493 Dihedral : 7.418 59.367 397 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 3.58 % Allowed : 14.66 % Favored : 81.76 % 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 (0.44), residues: 361 helix: 3.24 (0.32), residues: 229 sheet: 0.54 (0.80), residues: 42 loop : 0.10 (0.68), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 548 HIS 0.004 0.001 HIS B 708 PHE 0.009 0.001 PHE B 271 TYR 0.007 0.001 TYR B 740 ARG 0.001 0.000 ARG B 720 Details of bonding type rmsd hydrogen bonds : bond 0.04346 ( 206) hydrogen bonds : angle 3.46542 ( 612) covalent geometry : bond 0.00299 ( 2980) covalent geometry : angle 0.45050 ( 4039) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.313 Fit side-chains revert: symmetry clash REVERT: B 525 ASN cc_start: 0.7074 (OUTLIER) cc_final: 0.6812 (t0) REVERT: B 624 LYS cc_start: 0.8812 (mmtm) cc_final: 0.7859 (tmmt) outliers start: 11 outliers final: 9 residues processed: 91 average time/residue: 1.1812 time to fit residues: 110.1164 Evaluate side-chains 97 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 525 ASN Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 560 ILE Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 579 LYS Chi-restraints excluded: chain B residue 662 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 27 optimal weight: 0.0570 chunk 6 optimal weight: 1.9990 chunk 1 optimal weight: 10.0000 chunk 21 optimal weight: 0.0000 chunk 7 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 25 optimal weight: 0.4980 chunk 22 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.4302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 525 ASN B 531 GLN B 648 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.160519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.133713 restraints weight = 4034.774| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 1.67 r_work: 0.3739 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3599 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.3650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2980 Z= 0.107 Angle : 0.435 9.584 4039 Z= 0.220 Chirality : 0.039 0.127 491 Planarity : 0.002 0.028 493 Dihedral : 7.368 58.298 397 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 3.91 % Allowed : 15.31 % Favored : 80.78 % 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: 3.35 (0.44), residues: 361 helix: 3.30 (0.32), residues: 229 sheet: 0.50 (0.79), residues: 42 loop : 0.12 (0.69), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 548 HIS 0.003 0.001 HIS B 708 PHE 0.009 0.001 PHE B 572 TYR 0.006 0.001 TYR B 740 ARG 0.001 0.000 ARG B 720 Details of bonding type rmsd hydrogen bonds : bond 0.04075 ( 206) hydrogen bonds : angle 3.40496 ( 612) covalent geometry : bond 0.00223 ( 2980) covalent geometry : angle 0.43501 ( 4039) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.347 Fit side-chains revert: symmetry clash REVERT: B 525 ASN cc_start: 0.6907 (OUTLIER) cc_final: 0.6687 (t0) REVERT: B 624 LYS cc_start: 0.8812 (mmtm) cc_final: 0.7848 (tmmt) outliers start: 12 outliers final: 9 residues processed: 91 average time/residue: 1.1702 time to fit residues: 109.1388 Evaluate side-chains 97 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 525 ASN Chi-restraints excluded: chain B residue 543 MET Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 560 ILE Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 579 LYS Chi-restraints excluded: chain B residue 662 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 0.0870 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 0.5980 chunk 12 optimal weight: 10.0000 chunk 8 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 25 optimal weight: 0.0870 chunk 22 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.3936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 525 ASN B 531 GLN B 648 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.160979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.134302 restraints weight = 3978.339| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 1.66 r_work: 0.3743 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3608 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2980 Z= 0.104 Angle : 0.460 9.849 4039 Z= 0.227 Chirality : 0.039 0.152 491 Planarity : 0.002 0.028 493 Dihedral : 7.347 57.714 397 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 3.58 % Allowed : 16.61 % Favored : 79.80 % 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: 3.38 (0.44), residues: 361 helix: 3.34 (0.32), residues: 229 sheet: 0.47 (0.79), residues: 42 loop : 0.14 (0.69), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 548 HIS 0.003 0.000 HIS B 708 PHE 0.009 0.001 PHE B 572 TYR 0.006 0.001 TYR B 740 ARG 0.001 0.000 ARG B 720 Details of bonding type rmsd hydrogen bonds : bond 0.03965 ( 206) hydrogen bonds : angle 3.36258 ( 612) covalent geometry : bond 0.00216 ( 2980) covalent geometry : angle 0.46010 ( 4039) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4863.55 seconds wall clock time: 83 minutes 4.97 seconds (4984.97 seconds total)