Sun 23 Dec 22:22:43 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2gjg-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2gjg-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2gjg-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gjg-3.6-parrot-hancs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gjg-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gjg-3.6-parrot-hancs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Sun 23 Dec 22:22:52 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gjg-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gjg-3.6-parrot-hancs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 189 and 0 Target number of residues in the AU: 189 Target solvent content: 0.5933 Checking the provided sequence file Detected sequence length: 248 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 248 Adjusted target solvent content: 0.47 Input MTZ file: 2gjg-3.6-parrot-hancs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 5 Cell parameters: 89.350 48.920 57.630 90.000 93.310 90.000 Input sequence file: 2gjg-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 1984 target number of atoms Had to go as low as 0.65 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 3 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 Loops will be built when appropriate and at the last cycle Resolution range: 28.767 3.600 Wilson plot Bfac: 49.58 2918 reflections ( 97.99 % complete ) and 0 restraints for refining 2198 atoms. Observations/parameters ratio is 0.33 ------------------------------------------------------ Starting model: R = 0.3095 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2741 (Rfree = 0.000) for 2198 atoms. Found 14 (14 requested) and removed 33 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.15 3.28 Search for helices and strands: 0 residues in 0 chains, 2233 seeds are put forward Round 1: 122 peptides, 23 chains. Longest chain 11 peptides. Score 0.375 Round 2: 132 peptides, 23 chains. Longest chain 12 peptides. Score 0.437 Round 3: 139 peptides, 23 chains. Longest chain 13 peptides. Score 0.477 Round 4: 127 peptides, 19 chains. Longest chain 15 peptides. Score 0.507 Round 5: 127 peptides, 18 chains. Longest chain 14 peptides. Score 0.531 Taking the results from Round 5 Chains 18, Residues 109, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 2918 reflections ( 97.99 % complete ) and 4150 restraints for refining 1799 atoms. 3710 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2370 (Rfree = 0.000) for 1799 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 2: After refmac, R = 0.1968 (Rfree = 0.000) for 1791 atoms. Found 4 (11 requested) and removed 7 (5 requested) atoms. Cycle 3: After refmac, R = 0.1812 (Rfree = 0.000) for 1777 atoms. Found 6 (11 requested) and removed 11 (5 requested) atoms. Cycle 4: After refmac, R = 0.1632 (Rfree = 0.000) for 1767 atoms. Found 2 (11 requested) and removed 8 (5 requested) atoms. Cycle 5: After refmac, R = 0.1568 (Rfree = 0.000) for 1758 atoms. Found 2 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.07 3.20 Search for helices and strands: 0 residues in 0 chains, 1820 seeds are put forward Round 1: 122 peptides, 25 chains. Longest chain 7 peptides. Score 0.321 Round 2: 143 peptides, 24 chains. Longest chain 11 peptides. Score 0.476 Round 3: 145 peptides, 23 chains. Longest chain 11 peptides. Score 0.511 Round 4: 145 peptides, 21 chains. Longest chain 14 peptides. Score 0.556 Round 5: 154 peptides, 23 chains. Longest chain 13 peptides. Score 0.557 Taking the results from Round 5 Chains 23, Residues 131, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2918 reflections ( 97.99 % complete ) and 3994 restraints for refining 1799 atoms. 3493 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2016 (Rfree = 0.000) for 1799 atoms. Found 10 (11 requested) and removed 8 (5 requested) atoms. Cycle 7: After refmac, R = 0.1832 (Rfree = 0.000) for 1793 atoms. Found 2 (11 requested) and removed 8 (5 requested) atoms. Cycle 8: After refmac, R = 0.1762 (Rfree = 0.000) for 1786 atoms. Found 1 (11 requested) and removed 6 (5 requested) atoms. Cycle 9: After refmac, R = 0.1718 (Rfree = 0.000) for 1780 atoms. Found 4 (11 requested) and removed 7 (5 requested) atoms. Cycle 10: After refmac, R = 0.1680 (Rfree = 0.000) for 1777 atoms. Found 1 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.12 3.25 Search for helices and strands: 0 residues in 0 chains, 1819 seeds are put forward Round 1: 121 peptides, 23 chains. Longest chain 11 peptides. Score 0.369 Round 2: 139 peptides, 22 chains. Longest chain 17 peptides. Score 0.501 Round 3: 142 peptides, 23 chains. Longest chain 18 peptides. Score 0.494 Round 4: 145 peptides, 22 chains. Longest chain 13 peptides. Score 0.534 Round 5: 143 peptides, 21 chains. Longest chain 13 peptides. Score 0.546 Taking the results from Round 5 Chains 22, Residues 122, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 2918 reflections ( 97.99 % complete ) and 4006 restraints for refining 1799 atoms. 3506 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2101 (Rfree = 0.000) for 1799 atoms. Found 7 (11 requested) and removed 6 (5 requested) atoms. Cycle 12: After refmac, R = 0.1924 (Rfree = 0.000) for 1790 atoms. Found 6 (11 requested) and removed 7 (5 requested) atoms. Cycle 13: After refmac, R = 0.1836 (Rfree = 0.000) for 1786 atoms. Found 0 (11 requested) and removed 6 (5 requested) atoms. Cycle 14: After refmac, R = 0.1811 (Rfree = 0.000) for 1780 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 15: After refmac, R = 0.1803 (Rfree = 0.000) for 1774 atoms. Found 3 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.10 3.23 Search for helices and strands: 0 residues in 0 chains, 1818 seeds are put forward Round 1: 112 peptides, 21 chains. Longest chain 9 peptides. Score 0.365 Round 2: 128 peptides, 21 chains. Longest chain 15 peptides. Score 0.464 Round 3: 141 peptides, 23 chains. Longest chain 16 peptides. Score 0.489 Round 4: 125 peptides, 18 chains. Longest chain 20 peptides. Score 0.520 Round 5: 129 peptides, 16 chains. Longest chain 15 peptides. Score 0.587 Taking the results from Round 5 Chains 16, Residues 113, Estimated correctness of the model 9.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2918 reflections ( 97.99 % complete ) and 4161 restraints for refining 1799 atoms. 3725 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2221 (Rfree = 0.000) for 1799 atoms. Found 9 (11 requested) and removed 8 (5 requested) atoms. Cycle 17: After refmac, R = 0.2051 (Rfree = 0.000) for 1796 atoms. Found 3 (11 requested) and removed 6 (5 requested) atoms. Cycle 18: After refmac, R = 0.1960 (Rfree = 0.000) for 1793 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 19: After refmac, R = 0.1924 (Rfree = 0.000) for 1788 atoms. Found 3 (11 requested) and removed 6 (5 requested) atoms. Cycle 20: After refmac, R = 0.1879 (Rfree = 0.000) for 1784 atoms. Found 2 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.13 3.26 Search for helices and strands: 0 residues in 0 chains, 1826 seeds are put forward Round 1: 107 peptides, 21 chains. Longest chain 12 peptides. Score 0.332 Round 2: 120 peptides, 19 chains. Longest chain 13 peptides. Score 0.467 Round 3: 125 peptides, 19 chains. Longest chain 13 peptides. Score 0.496 Round 4: 122 peptides, 19 chains. Longest chain 13 peptides. Score 0.479 Round 5: 123 peptides, 19 chains. Longest chain 16 peptides. Score 0.485 Taking the results from Round 3 Chains 20, Residues 106, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 2918 reflections ( 97.99 % complete ) and 4018 restraints for refining 1799 atoms. 3588 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2022 (Rfree = 0.000) for 1799 atoms. Found 5 (11 requested) and removed 6 (5 requested) atoms. Cycle 22: After refmac, R = 0.1913 (Rfree = 0.000) for 1795 atoms. Found 1 (11 requested) and removed 7 (5 requested) atoms. Cycle 23: After refmac, R = 0.1876 (Rfree = 0.000) for 1788 atoms. Found 3 (11 requested) and removed 7 (5 requested) atoms. Cycle 24: After refmac, R = 0.1846 (Rfree = 0.000) for 1782 atoms. Found 2 (11 requested) and removed 5 (5 requested) atoms. Cycle 25: After refmac, R = 0.1823 (Rfree = 0.000) for 1778 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.12 3.25 Search for helices and strands: 0 residues in 0 chains, 1816 seeds are put forward Round 1: 115 peptides, 24 chains. Longest chain 8 peptides. Score 0.302 Round 2: 117 peptides, 19 chains. Longest chain 11 peptides. Score 0.450 Round 3: 118 peptides, 21 chains. Longest chain 11 peptides. Score 0.403 Round 4: 131 peptides, 20 chains. Longest chain 16 peptides. Score 0.505 Round 5: 125 peptides, 22 chains. Longest chain 12 peptides. Score 0.420 Taking the results from Round 4 Chains 20, Residues 111, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 2918 reflections ( 97.99 % complete ) and 4077 restraints for refining 1799 atoms. 3630 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1993 (Rfree = 0.000) for 1799 atoms. Found 11 (11 requested) and removed 7 (5 requested) atoms. Cycle 27: After refmac, R = 0.1823 (Rfree = 0.000) for 1799 atoms. Found 6 (11 requested) and removed 8 (5 requested) atoms. Cycle 28: After refmac, R = 0.1751 (Rfree = 0.000) for 1793 atoms. Found 3 (11 requested) and removed 5 (5 requested) atoms. Cycle 29: After refmac, R = 0.1759 (Rfree = 0.000) for 1789 atoms. Found 2 (11 requested) and removed 5 (5 requested) atoms. Cycle 30: After refmac, R = 0.1646 (Rfree = 0.000) for 1786 atoms. Found 2 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.11 3.24 Search for helices and strands: 0 residues in 0 chains, 1826 seeds are put forward Round 1: 99 peptides, 18 chains. Longest chain 9 peptides. Score 0.363 Round 2: 106 peptides, 19 chains. Longest chain 10 peptides. Score 0.381 Round 3: 116 peptides, 18 chains. Longest chain 13 peptides. Score 0.469 Round 4: 122 peptides, 20 chains. Longest chain 16 peptides. Score 0.454 Round 5: 120 peptides, 18 chains. Longest chain 12 peptides. Score 0.492 Taking the results from Round 5 Chains 18, Residues 102, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2918 reflections ( 97.99 % complete ) and 4178 restraints for refining 1799 atoms. 3788 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1862 (Rfree = 0.000) for 1799 atoms. Found 3 (11 requested) and removed 6 (5 requested) atoms. Cycle 32: After refmac, R = 0.1734 (Rfree = 0.000) for 1789 atoms. Found 3 (11 requested) and removed 6 (5 requested) atoms. Cycle 33: After refmac, R = 0.1684 (Rfree = 0.000) for 1784 atoms. Found 1 (11 requested) and removed 5 (5 requested) atoms. Cycle 34: After refmac, R = 0.1646 (Rfree = 0.000) for 1780 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 35: After refmac, R = 0.1625 (Rfree = 0.000) for 1775 atoms. Found 2 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.13 3.26 Search for helices and strands: 0 residues in 0 chains, 1792 seeds are put forward Round 1: 105 peptides, 21 chains. Longest chain 10 peptides. Score 0.318 Round 2: 120 peptides, 21 chains. Longest chain 12 peptides. Score 0.416 Round 3: 125 peptides, 22 chains. Longest chain 12 peptides. Score 0.420 Round 4: 130 peptides, 21 chains. Longest chain 13 peptides. Score 0.475 Round 5: 139 peptides, 23 chains. Longest chain 14 peptides. Score 0.477 Taking the results from Round 5 Chains 23, Residues 116, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2918 reflections ( 97.99 % complete ) and 4120 restraints for refining 1798 atoms. 3679 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1947 (Rfree = 0.000) for 1798 atoms. Found 10 (11 requested) and removed 5 (5 requested) atoms. Cycle 37: After refmac, R = 0.1796 (Rfree = 0.000) for 1800 atoms. Found 1 (11 requested) and removed 7 (5 requested) atoms. Cycle 38: After refmac, R = 0.1784 (Rfree = 0.000) for 1793 atoms. Found 4 (11 requested) and removed 5 (5 requested) atoms. Cycle 39: After refmac, R = 0.1747 (Rfree = 0.000) for 1791 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 40: After refmac, R = 0.1718 (Rfree = 0.000) for 1786 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.15 3.28 Search for helices and strands: 0 residues in 0 chains, 1807 seeds are put forward Round 1: 114 peptides, 23 chains. Longest chain 7 peptides. Score 0.323 Round 2: 122 peptides, 22 chains. Longest chain 9 peptides. Score 0.402 Round 3: 118 peptides, 18 chains. Longest chain 12 peptides. Score 0.481 Round 4: 128 peptides, 20 chains. Longest chain 14 peptides. Score 0.488 Round 5: 117 peptides, 20 chains. Longest chain 13 peptides. Score 0.423 Taking the results from Round 4 Chains 20, Residues 108, Estimated correctness of the model 0.0 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 2918 reflections ( 97.99 % complete ) and 4019 restraints for refining 1799 atoms. 3570 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2017 (Rfree = 0.000) for 1799 atoms. Found 10 (11 requested) and removed 8 (5 requested) atoms. Cycle 42: After refmac, R = 0.1876 (Rfree = 0.000) for 1793 atoms. Found 3 (11 requested) and removed 7 (5 requested) atoms. Cycle 43: After refmac, R = 0.1796 (Rfree = 0.000) for 1788 atoms. Found 3 (11 requested) and removed 7 (5 requested) atoms. Cycle 44: After refmac, R = 0.1755 (Rfree = 0.000) for 1781 atoms. Found 1 (11 requested) and removed 5 (5 requested) atoms. Cycle 45: After refmac, R = 0.1727 (Rfree = 0.000) for 1775 atoms. Found 2 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.10 3.23 Search for helices and strands: 0 residues in 0 chains, 1804 seeds are put forward Round 1: 84 peptides, 16 chains. Longest chain 8 peptides. Score 0.319 Round 2: 108 peptides, 18 chains. Longest chain 14 peptides. Score 0.421 Round 3: 115 peptides, 17 chains. Longest chain 15 peptides. Score 0.489 Round 4: 111 peptides, 18 chains. Longest chain 10 peptides. Score 0.440 Round 5: 110 peptides, 19 chains. Longest chain 10 peptides. Score 0.407 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 17, Residues 98, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence Sequence coverage is 8 % Consider running further cycles of model building using 2gjg-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2918 reflections ( 97.99 % complete ) and 4152 restraints for refining 1799 atoms. 3756 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1848 (Rfree = 0.000) for 1799 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.1764 (Rfree = 0.000) for 1789 atoms. Found 0 (11 requested) and removed 2 (5 requested) atoms. Cycle 48: After refmac, R = 0.1741 (Rfree = 0.000) for 1787 atoms. Found 0 (11 requested) and removed 1 (5 requested) atoms. Cycle 49: After refmac, R = 0.1715 (Rfree = 0.000) for 1786 atoms. Found 0 (11 requested) and removed 0 (5 requested) atoms. TimeTaking 31.12