Starting phenix.real_space_refine on Thu Jul 24 05:45:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gim_51374/07_2025/9gim_51374.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gim_51374/07_2025/9gim_51374.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9gim_51374/07_2025/9gim_51374.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gim_51374/07_2025/9gim_51374.map" model { file = "/net/cci-nas-00/data/ceres_data/9gim_51374/07_2025/9gim_51374.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gim_51374/07_2025/9gim_51374.cif" } resolution = 4.11 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= 1.000 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 22 5.16 5 C 3410 2.51 5 N 918 2.21 5 O 971 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 5321 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 639, 5321 Classifications: {'peptide': 639} Link IDs: {'PTRANS': 40, 'TRANS': 598} Chain breaks: 2 Time building chain proxies: 4.23, per 1000 atoms: 0.79 Number of scatterers: 5321 At special positions: 0 Unit cell: (75.024, 79.192, 114.203, 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 22 16.00 O 971 8.00 N 918 7.00 C 3410 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: 1.30 Conformation dependent library (CDL) restraints added in 641.0 milliseconds 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1212 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 9 sheets defined 36.0% alpha, 16.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 232 through 252 removed outlier: 3.677A pdb=" N ARG A 238 " --> pdb=" O ASP A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 588 removed outlier: 3.543A pdb=" N LYS A 580 " --> pdb=" O GLU A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 613 removed outlier: 3.553A pdb=" N SER A 611 " --> pdb=" O ILE A 607 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG A 613 " --> pdb=" O GLU A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 626 removed outlier: 3.691A pdb=" N VAL A 623 " --> pdb=" O ARG A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 656 Processing helix chain 'A' and resid 657 through 661 Processing helix chain 'A' and resid 678 through 683 removed outlier: 3.894A pdb=" N CYS A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 704 removed outlier: 3.573A pdb=" N TYR A 689 " --> pdb=" O ASP A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 720 removed outlier: 3.735A pdb=" N TYR A 716 " --> pdb=" O ILE A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 730 Processing helix chain 'A' and resid 733 through 746 Processing helix chain 'A' and resid 747 through 751 removed outlier: 3.970A pdb=" N GLU A 750 " --> pdb=" O ASP A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 777 Processing helix chain 'A' and resid 783 through 796 Processing helix chain 'A' and resid 800 through 813 Processing helix chain 'A' and resid 816 through 820 removed outlier: 3.576A pdb=" N LEU A 819 " --> pdb=" O PRO A 816 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE A 820 " --> pdb=" O ILE A 817 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 816 through 820' Processing helix chain 'A' and resid 827 through 834 Processing helix chain 'A' and resid 839 through 846 Processing helix chain 'A' and resid 857 through 870 Processing helix chain 'A' and resid 871 through 884 Processing helix chain 'A' and resid 892 through 895 removed outlier: 3.975A pdb=" N GLU A 895 " --> pdb=" O GLY A 892 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 892 through 895' Processing helix chain 'A' and resid 933 through 947 Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 82 removed outlier: 6.893A pdb=" N ARG A 147 " --> pdb=" O VAL A 27 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N GLY A 29 " --> pdb=" O PHE A 145 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N PHE A 145 " --> pdb=" O GLY A 29 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 57 through 63 removed outlier: 7.094A pdb=" N GLU A 57 " --> pdb=" O VAL A 51 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N VAL A 51 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL A 45 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ASP A 95 " --> pdb=" O PHE A 104 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N PHE A 104 " --> pdb=" O ASP A 95 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 199 through 203 Processing sheet with id=AA4, first strand: chain 'A' and resid 534 through 539 removed outlier: 3.797A pdb=" N ILE A 553 " --> pdb=" O ASP A 548 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 598 through 602 Processing sheet with id=AA6, first strand: chain 'A' and resid 663 through 665 Processing sheet with id=AA7, first strand: chain 'A' and resid 757 through 761 Processing sheet with id=AA8, first strand: chain 'A' and resid 847 through 849 Processing sheet with id=AA9, first strand: chain 'A' and resid 897 through 898 removed outlier: 3.744A pdb=" N GLY A 901 " --> pdb=" O GLY A 898 " (cutoff:3.500A) 208 hydrogen bonds defined for protein. 573 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: 1.69 Time building geometry restraints manager: 1.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1748 1.34 - 1.46: 1173 1.46 - 1.58: 2505 1.58 - 1.69: 0 1.69 - 1.81: 39 Bond restraints: 5465 Sorted by residual: bond pdb=" CB PRO A 72 " pdb=" CG PRO A 72 " ideal model delta sigma weight residual 1.492 1.530 -0.038 5.00e-02 4.00e+02 5.81e-01 bond pdb=" C MET A 153 " pdb=" N PRO A 154 " ideal model delta sigma weight residual 1.329 1.338 -0.008 1.25e-02 6.40e+03 4.49e-01 bond pdb=" CA VAL A 27 " pdb=" CB VAL A 27 " ideal model delta sigma weight residual 1.545 1.539 0.006 9.10e-03 1.21e+04 4.28e-01 bond pdb=" CA VAL A 229 " pdb=" CB VAL A 229 " ideal model delta sigma weight residual 1.540 1.549 -0.009 1.36e-02 5.41e+03 4.04e-01 bond pdb=" CB TRP A 74 " pdb=" CG TRP A 74 " ideal model delta sigma weight residual 1.498 1.479 0.019 3.10e-02 1.04e+03 3.94e-01 ... (remaining 5460 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.03: 7109 1.03 - 2.05: 213 2.05 - 3.08: 59 3.08 - 4.11: 9 4.11 - 5.13: 5 Bond angle restraints: 7395 Sorted by residual: angle pdb=" C ASP A 228 " pdb=" N VAL A 229 " pdb=" CA VAL A 229 " ideal model delta sigma weight residual 121.97 125.75 -3.78 1.80e+00 3.09e-01 4.40e+00 angle pdb=" N THR A 121 " pdb=" CA THR A 121 " pdb=" CB THR A 121 " ideal model delta sigma weight residual 113.65 110.66 2.99 1.47e+00 4.63e-01 4.13e+00 angle pdb=" C ARG A 560 " pdb=" N LEU A 561 " pdb=" CA LEU A 561 " ideal model delta sigma weight residual 121.54 125.34 -3.80 1.91e+00 2.74e-01 3.96e+00 angle pdb=" N MET A 153 " pdb=" CA MET A 153 " pdb=" C MET A 153 " ideal model delta sigma weight residual 109.81 114.08 -4.27 2.21e+00 2.05e-01 3.73e+00 angle pdb=" C VAL A 26 " pdb=" N VAL A 27 " pdb=" CA VAL A 27 " ideal model delta sigma weight residual 122.97 121.09 1.88 9.80e-01 1.04e+00 3.68e+00 ... (remaining 7390 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.37: 2894 10.37 - 20.73: 269 20.73 - 31.10: 82 31.10 - 41.46: 38 41.46 - 51.83: 7 Dihedral angle restraints: 3290 sinusoidal: 1414 harmonic: 1876 Sorted by residual: dihedral pdb=" CA MET A 153 " pdb=" C MET A 153 " pdb=" N PRO A 154 " pdb=" CA PRO A 154 " ideal model delta harmonic sigma weight residual -180.00 -162.72 -17.28 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA HIS A 549 " pdb=" C HIS A 549 " pdb=" N ASN A 550 " pdb=" CA ASN A 550 " ideal model delta harmonic sigma weight residual 180.00 164.41 15.59 0 5.00e+00 4.00e-02 9.73e+00 dihedral pdb=" CA LEU A 835 " pdb=" CB LEU A 835 " pdb=" CG LEU A 835 " pdb=" CD1 LEU A 835 " ideal model delta sinusoidal sigma weight residual 180.00 128.63 51.37 3 1.50e+01 4.44e-03 9.01e+00 ... (remaining 3287 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 418 0.026 - 0.051: 245 0.051 - 0.077: 50 0.077 - 0.102: 34 0.102 - 0.128: 17 Chirality restraints: 764 Sorted by residual: chirality pdb=" CA ILE A 566 " pdb=" N ILE A 566 " pdb=" C ILE A 566 " pdb=" CB ILE A 566 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.08e-01 chirality pdb=" CA VAL A 24 " pdb=" N VAL A 24 " pdb=" C VAL A 24 " pdb=" CB VAL A 24 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.02e-01 chirality pdb=" CB VAL A 229 " pdb=" CA VAL A 229 " pdb=" CG1 VAL A 229 " pdb=" CG2 VAL A 229 " both_signs ideal model delta sigma weight residual False -2.63 -2.51 -0.12 2.00e-01 2.50e+01 3.75e-01 ... (remaining 761 not shown) Planarity restraints: 968 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 528 " 0.031 5.00e-02 4.00e+02 4.69e-02 3.52e+00 pdb=" N PRO A 529 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 529 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 529 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 594 " -0.025 5.00e-02 4.00e+02 3.85e-02 2.37e+00 pdb=" N PRO A 595 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 595 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 595 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 857 " 0.022 5.00e-02 4.00e+02 3.32e-02 1.76e+00 pdb=" N PRO A 858 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 858 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 858 " 0.019 5.00e-02 4.00e+02 ... (remaining 965 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1020 2.77 - 3.31: 5123 3.31 - 3.84: 8349 3.84 - 4.37: 9504 4.37 - 4.90: 16324 Nonbonded interactions: 40320 Sorted by model distance: nonbonded pdb=" NH1 ARG A 253 " pdb=" OD1 ASP A 258 " model vdw 2.242 3.120 nonbonded pdb=" OH TYR A 612 " pdb=" OG SER A 688 " model vdw 2.253 3.040 nonbonded pdb=" O ARG A 248 " pdb=" OG SER A 251 " model vdw 2.291 3.040 nonbonded pdb=" OH TYR A 849 " pdb=" NE1 TRP A 864 " model vdw 2.301 3.120 nonbonded pdb=" OE2 GLU A 535 " pdb=" NE2 HIS A 549 " model vdw 2.338 3.120 ... (remaining 40315 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: 3.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 17.520 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 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 : 0.002 0.038 5465 Z= 0.108 Angle : 0.479 5.133 7395 Z= 0.250 Chirality : 0.038 0.128 764 Planarity : 0.004 0.047 968 Dihedral : 10.035 51.827 2078 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.64 % Favored : 93.21 % Rotamer: Outliers : 1.71 % Allowed : 4.79 % Favored : 93.49 % 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: -0.64 (0.34), residues: 633 helix: 0.55 (0.37), residues: 190 sheet: -0.26 (0.44), residues: 121 loop : -1.06 (0.37), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 862 HIS 0.003 0.001 HIS A 857 PHE 0.015 0.001 PHE A 692 TYR 0.006 0.001 TYR A 44 ARG 0.002 0.000 ARG A 537 Details of bonding type rmsd hydrogen bonds : bond 0.14919 ( 208) hydrogen bonds : angle 5.93364 ( 573) covalent geometry : bond 0.00240 ( 5465) covalent geometry : angle 0.47934 ( 7395) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 563 ASN cc_start: 0.7797 (t0) cc_final: 0.7426 (t0) outliers start: 10 outliers final: 7 residues processed: 76 average time/residue: 0.2101 time to fit residues: 20.2973 Evaluate side-chains 57 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 53 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 36 optimal weight: 0.0980 chunk 57 optimal weight: 0.6980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN A 71 ASN ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 GLN A 254 HIS A 603 HIS A 767 GLN A 861 GLN A 891 ASN A 909 GLN A 924 ASN A 949 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.111094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.087409 restraints weight = 13099.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.086771 restraints weight = 15220.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.087923 restraints weight = 12122.093| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5465 Z= 0.176 Angle : 0.592 9.821 7395 Z= 0.304 Chirality : 0.042 0.152 764 Planarity : 0.004 0.045 968 Dihedral : 4.066 26.445 709 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.27 % Favored : 92.58 % Rotamer: Outliers : 0.17 % Allowed : 2.40 % Favored : 97.43 % 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: -0.90 (0.33), residues: 633 helix: 0.27 (0.36), residues: 193 sheet: -0.43 (0.45), residues: 125 loop : -1.19 (0.37), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 74 HIS 0.005 0.001 HIS A 857 PHE 0.020 0.002 PHE A 692 TYR 0.019 0.001 TYR A 152 ARG 0.004 0.000 ARG A 695 Details of bonding type rmsd hydrogen bonds : bond 0.04269 ( 208) hydrogen bonds : angle 5.26213 ( 573) covalent geometry : bond 0.00414 ( 5465) covalent geometry : angle 0.59182 ( 7395) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 62 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 563 ASN cc_start: 0.7869 (t0) cc_final: 0.7506 (t0) REVERT: A 582 ASP cc_start: 0.6747 (t0) cc_final: 0.6512 (t70) outliers start: 1 outliers final: 0 residues processed: 63 average time/residue: 0.1780 time to fit residues: 15.0147 Evaluate side-chains 50 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 4 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 52 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 803 GLN A 826 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.108574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.084531 restraints weight = 13148.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.083740 restraints weight = 12844.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.083990 restraints weight = 10998.742| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 5465 Z= 0.218 Angle : 0.629 9.030 7395 Z= 0.320 Chirality : 0.043 0.132 764 Planarity : 0.004 0.044 968 Dihedral : 4.359 28.259 709 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.11 % Favored : 92.73 % Rotamer: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % 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: -1.18 (0.33), residues: 633 helix: 0.01 (0.35), residues: 193 sheet: -0.69 (0.44), residues: 127 loop : -1.28 (0.37), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 74 HIS 0.006 0.001 HIS A 857 PHE 0.028 0.002 PHE A 692 TYR 0.022 0.001 TYR A 849 ARG 0.003 0.000 ARG A 877 Details of bonding type rmsd hydrogen bonds : bond 0.04141 ( 208) hydrogen bonds : angle 5.46808 ( 573) covalent geometry : bond 0.00512 ( 5465) covalent geometry : angle 0.62901 ( 7395) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.5928 (mpp) cc_final: 0.5517 (mmt) REVERT: A 563 ASN cc_start: 0.7905 (t0) cc_final: 0.7575 (t0) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1775 time to fit residues: 13.0260 Evaluate side-chains 43 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 12 optimal weight: 4.9990 chunk 43 optimal weight: 0.6980 chunk 1 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 7 optimal weight: 7.9990 chunk 34 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.109331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.086369 restraints weight = 13443.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.085193 restraints weight = 11947.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.085555 restraints weight = 10588.013| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 5465 Z= 0.205 Angle : 0.624 9.872 7395 Z= 0.317 Chirality : 0.042 0.128 764 Planarity : 0.004 0.046 968 Dihedral : 4.512 29.629 709 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.42 % Favored : 92.42 % Rotamer: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % 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: -1.32 (0.33), residues: 633 helix: -0.12 (0.35), residues: 193 sheet: -0.63 (0.46), residues: 125 loop : -1.42 (0.36), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 74 HIS 0.006 0.001 HIS A 857 PHE 0.025 0.002 PHE A 692 TYR 0.014 0.001 TYR A 849 ARG 0.003 0.000 ARG A 537 Details of bonding type rmsd hydrogen bonds : bond 0.03974 ( 208) hydrogen bonds : angle 5.45381 ( 573) covalent geometry : bond 0.00490 ( 5465) covalent geometry : angle 0.62382 ( 7395) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.691 Fit side-chains revert: symmetry clash REVERT: A 122 MET cc_start: 0.5415 (mpp) cc_final: 0.4775 (mpp) REVERT: A 153 MET cc_start: 0.6306 (mtt) cc_final: 0.5012 (mtt) REVERT: A 563 ASN cc_start: 0.7839 (t0) cc_final: 0.7504 (t0) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.1819 time to fit residues: 14.4568 Evaluate side-chains 41 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 30 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 6 optimal weight: 6.9990 chunk 40 optimal weight: 0.0020 chunk 24 optimal weight: 0.2980 chunk 27 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.111076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.088074 restraints weight = 13074.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.087727 restraints weight = 11117.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.087598 restraints weight = 10205.895| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5465 Z= 0.117 Angle : 0.541 9.224 7395 Z= 0.272 Chirality : 0.040 0.182 764 Planarity : 0.004 0.049 968 Dihedral : 4.243 27.711 709 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.69 % Favored : 94.15 % Rotamer: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % 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: -1.06 (0.33), residues: 633 helix: 0.34 (0.37), residues: 193 sheet: -0.66 (0.46), residues: 125 loop : -1.36 (0.36), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 74 HIS 0.002 0.001 HIS A 549 PHE 0.016 0.001 PHE A 692 TYR 0.010 0.001 TYR A 849 ARG 0.002 0.000 ARG A 575 Details of bonding type rmsd hydrogen bonds : bond 0.03359 ( 208) hydrogen bonds : angle 5.13191 ( 573) covalent geometry : bond 0.00274 ( 5465) covalent geometry : angle 0.54098 ( 7395) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.586 Fit side-chains revert: symmetry clash REVERT: A 122 MET cc_start: 0.5226 (mpp) cc_final: 0.4730 (mpp) REVERT: A 153 MET cc_start: 0.6244 (mtt) cc_final: 0.5773 (mtt) REVERT: A 563 ASN cc_start: 0.7813 (t0) cc_final: 0.7493 (t0) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.1693 time to fit residues: 13.0333 Evaluate side-chains 41 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 18 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 24 optimal weight: 0.0470 chunk 20 optimal weight: 0.7980 chunk 8 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 overall best weight: 0.7680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.110600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.086416 restraints weight = 13177.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.086087 restraints weight = 12851.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.086654 restraints weight = 10820.240| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5465 Z= 0.141 Angle : 0.561 9.230 7395 Z= 0.284 Chirality : 0.041 0.134 764 Planarity : 0.004 0.050 968 Dihedral : 4.295 26.898 709 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.95 % Favored : 92.89 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % 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: -1.02 (0.34), residues: 633 helix: 0.42 (0.37), residues: 187 sheet: -0.68 (0.46), residues: 125 loop : -1.33 (0.36), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 864 HIS 0.003 0.001 HIS A 857 PHE 0.026 0.002 PHE A 648 TYR 0.009 0.001 TYR A 79 ARG 0.002 0.000 ARG A 844 Details of bonding type rmsd hydrogen bonds : bond 0.03393 ( 208) hydrogen bonds : angle 5.19391 ( 573) covalent geometry : bond 0.00335 ( 5465) covalent geometry : angle 0.56066 ( 7395) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.685 Fit side-chains revert: symmetry clash REVERT: A 92 GLU cc_start: 0.6440 (mp0) cc_final: 0.6219 (mp0) REVERT: A 122 MET cc_start: 0.5073 (mpp) cc_final: 0.4538 (mpp) REVERT: A 563 ASN cc_start: 0.7831 (t0) cc_final: 0.7503 (t0) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.1579 time to fit residues: 12.3783 Evaluate side-chains 42 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 45 optimal weight: 9.9990 chunk 20 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 60 optimal weight: 0.0470 chunk 16 optimal weight: 4.9990 chunk 36 optimal weight: 0.5980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.111126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.088748 restraints weight = 13126.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.087413 restraints weight = 12566.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.087823 restraints weight = 11875.944| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5465 Z= 0.119 Angle : 0.539 8.930 7395 Z= 0.272 Chirality : 0.040 0.172 764 Planarity : 0.004 0.050 968 Dihedral : 4.308 32.397 709 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.69 % Favored : 94.15 % Rotamer: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.56 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.34), residues: 633 helix: 0.54 (0.37), residues: 187 sheet: -0.73 (0.45), residues: 127 loop : -1.33 (0.36), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 74 HIS 0.003 0.001 HIS A 857 PHE 0.017 0.001 PHE A 692 TYR 0.011 0.001 TYR A 152 ARG 0.002 0.000 ARG A 81 Details of bonding type rmsd hydrogen bonds : bond 0.03160 ( 208) hydrogen bonds : angle 5.06344 ( 573) covalent geometry : bond 0.00280 ( 5465) covalent geometry : angle 0.53866 ( 7395) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.655 Fit side-chains revert: symmetry clash REVERT: A 122 MET cc_start: 0.4764 (mpp) cc_final: 0.2841 (mtp) REVERT: A 563 ASN cc_start: 0.7777 (t0) cc_final: 0.7468 (t0) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.1642 time to fit residues: 12.7309 Evaluate side-chains 43 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 40 optimal weight: 0.0970 chunk 38 optimal weight: 0.9990 chunk 50 optimal weight: 0.2980 chunk 45 optimal weight: 7.9990 chunk 43 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 28 optimal weight: 0.3980 chunk 21 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 803 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.111676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.089525 restraints weight = 13172.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.087568 restraints weight = 12176.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.088126 restraints weight = 10554.653| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5465 Z= 0.118 Angle : 0.581 12.784 7395 Z= 0.288 Chirality : 0.041 0.184 764 Planarity : 0.004 0.050 968 Dihedral : 4.310 31.049 709 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.85 % Favored : 94.00 % Rotamer: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.56 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.34), residues: 633 helix: 0.63 (0.38), residues: 187 sheet: -0.67 (0.45), residues: 127 loop : -1.32 (0.37), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 74 HIS 0.003 0.001 HIS A 857 PHE 0.016 0.001 PHE A 881 TYR 0.008 0.001 TYR A 79 ARG 0.001 0.000 ARG A 695 Details of bonding type rmsd hydrogen bonds : bond 0.03124 ( 208) hydrogen bonds : angle 4.98170 ( 573) covalent geometry : bond 0.00277 ( 5465) covalent geometry : angle 0.58094 ( 7395) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.616 Fit side-chains revert: symmetry clash REVERT: A 122 MET cc_start: 0.4131 (mpp) cc_final: 0.3192 (mtm) REVERT: A 563 ASN cc_start: 0.7832 (t0) cc_final: 0.7508 (t0) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.1634 time to fit residues: 12.1899 Evaluate side-chains 42 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 24 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 1 optimal weight: 0.0470 chunk 11 optimal weight: 0.4980 chunk 42 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 12 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.111844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.089640 restraints weight = 13191.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.087838 restraints weight = 13990.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.088708 restraints weight = 12392.080| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5465 Z= 0.118 Angle : 0.564 8.862 7395 Z= 0.283 Chirality : 0.041 0.158 764 Planarity : 0.004 0.050 968 Dihedral : 4.292 28.267 709 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.00 % Favored : 93.84 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % 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: -0.93 (0.34), residues: 633 helix: 0.63 (0.37), residues: 187 sheet: -0.71 (0.45), residues: 125 loop : -1.33 (0.36), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 74 HIS 0.003 0.001 HIS A 857 PHE 0.015 0.001 PHE A 881 TYR 0.009 0.001 TYR A 152 ARG 0.001 0.000 ARG A 695 Details of bonding type rmsd hydrogen bonds : bond 0.03102 ( 208) hydrogen bonds : angle 4.97787 ( 573) covalent geometry : bond 0.00279 ( 5465) covalent geometry : angle 0.56406 ( 7395) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.642 Fit side-chains revert: symmetry clash REVERT: A 122 MET cc_start: 0.4278 (mpp) cc_final: 0.3151 (mtm) REVERT: A 563 ASN cc_start: 0.7741 (t0) cc_final: 0.7429 (t0) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1660 time to fit residues: 12.6633 Evaluate side-chains 41 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 11 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 33 optimal weight: 0.4980 chunk 30 optimal weight: 0.8980 chunk 49 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.111148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.088878 restraints weight = 13339.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.087154 restraints weight = 12467.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.087597 restraints weight = 10590.035| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5465 Z= 0.140 Angle : 0.600 8.876 7395 Z= 0.300 Chirality : 0.041 0.161 764 Planarity : 0.004 0.050 968 Dihedral : 4.371 27.727 709 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.32 % Favored : 93.52 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % 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: -1.06 (0.34), residues: 633 helix: 0.42 (0.37), residues: 193 sheet: -0.74 (0.45), residues: 125 loop : -1.39 (0.37), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 74 HIS 0.003 0.001 HIS A 857 PHE 0.018 0.001 PHE A 692 TYR 0.008 0.001 TYR A 849 ARG 0.009 0.000 ARG A 81 Details of bonding type rmsd hydrogen bonds : bond 0.03208 ( 208) hydrogen bonds : angle 5.03474 ( 573) covalent geometry : bond 0.00330 ( 5465) covalent geometry : angle 0.60046 ( 7395) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.548 Fit side-chains revert: symmetry clash REVERT: A 122 MET cc_start: 0.4366 (mpp) cc_final: 0.3226 (mtm) REVERT: A 563 ASN cc_start: 0.7789 (t0) cc_final: 0.7462 (t0) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.1502 time to fit residues: 11.9994 Evaluate side-chains 40 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 47 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 37 optimal weight: 0.0270 chunk 39 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 38 optimal weight: 0.3980 chunk 55 optimal weight: 0.5980 chunk 18 optimal weight: 0.0870 chunk 46 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 overall best weight: 0.3416 ------------------------------------------------------------------------------- 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 = 0.3678 r_free = 0.3678 target = 0.112269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.090386 restraints weight = 13323.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.088834 restraints weight = 14079.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.089670 restraints weight = 13332.398| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 5465 Z= 0.104 Angle : 0.572 8.697 7395 Z= 0.283 Chirality : 0.041 0.179 764 Planarity : 0.004 0.051 968 Dihedral : 4.218 26.724 709 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.06 % Favored : 94.79 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % 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: -0.86 (0.34), residues: 633 helix: 0.87 (0.38), residues: 187 sheet: -0.78 (0.44), residues: 125 loop : -1.36 (0.36), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 74 HIS 0.002 0.001 HIS A 214 PHE 0.015 0.001 PHE A 881 TYR 0.007 0.001 TYR A 79 ARG 0.006 0.000 ARG A 81 Details of bonding type rmsd hydrogen bonds : bond 0.02931 ( 208) hydrogen bonds : angle 4.85129 ( 573) covalent geometry : bond 0.00241 ( 5465) covalent geometry : angle 0.57216 ( 7395) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1980.51 seconds wall clock time: 35 minutes 10.01 seconds (2110.01 seconds total)