Sun 23 Dec 22:23:08 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-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2gjg-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2gjg-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gjg-3.4-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-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gjg-3.4-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 22:23:18 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-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gjg-3.4-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 192 and 0 Target number of residues in the AU: 192 Target solvent content: 0.5868 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-3.4-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-3.4-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 3.401 Wilson plot Bfac: 46.89 3446 reflections ( 98.15 % complete ) and 0 restraints for refining 2197 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Starting model: R = 0.3032 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2364 (Rfree = 0.000) for 2197 atoms. Found 10 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.13 3.26 Search for helices and strands: 0 residues in 0 chains, 2226 seeds are put forward Round 1: 125 peptides, 24 chains. Longest chain 9 peptides. Score 0.367 Round 2: 126 peptides, 18 chains. Longest chain 15 peptides. Score 0.526 Round 3: 137 peptides, 19 chains. Longest chain 18 peptides. Score 0.560 Round 4: 145 peptides, 16 chains. Longest chain 22 peptides. Score 0.659 Round 5: 151 peptides, 18 chains. Longest chain 28 peptides. Score 0.646 Taking the results from Round 4 Chains 16, Residues 129, Estimated correctness of the model 46.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3446 reflections ( 98.15 % complete ) and 3878 restraints for refining 1804 atoms. 3378 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2253 (Rfree = 0.000) for 1804 atoms. Found 11 (13 requested) and removed 12 (6 requested) atoms. Cycle 2: After refmac, R = 0.2010 (Rfree = 0.000) for 1791 atoms. Found 6 (13 requested) and removed 8 (6 requested) atoms. Cycle 3: After refmac, R = 0.1903 (Rfree = 0.000) for 1785 atoms. Found 2 (13 requested) and removed 7 (6 requested) atoms. Cycle 4: After refmac, R = 0.1908 (Rfree = 0.000) for 1779 atoms. Found 6 (13 requested) and removed 6 (6 requested) atoms. Cycle 5: After refmac, R = 0.1826 (Rfree = 0.000) for 1778 atoms. Found 4 (13 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.96 3.08 Search for helices and strands: 0 residues in 0 chains, 1834 seeds are put forward Round 1: 120 peptides, 22 chains. Longest chain 14 peptides. Score 0.389 Round 2: 142 peptides, 21 chains. Longest chain 14 peptides. Score 0.541 Round 3: 142 peptides, 20 chains. Longest chain 17 peptides. Score 0.563 Round 4: 152 peptides, 21 chains. Longest chain 16 peptides. Score 0.590 Round 5: 136 peptides, 18 chains. Longest chain 13 peptides. Score 0.577 Taking the results from Round 4 Chains 21, Residues 131, Estimated correctness of the model 25.3 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 3446 reflections ( 98.15 % complete ) and 3818 restraints for refining 1804 atoms. 3283 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2164 (Rfree = 0.000) for 1804 atoms. Found 7 (13 requested) and removed 9 (6 requested) atoms. Cycle 7: After refmac, R = 0.1967 (Rfree = 0.000) for 1796 atoms. Found 5 (13 requested) and removed 10 (6 requested) atoms. Cycle 8: After refmac, R = 0.1995 (Rfree = 0.000) for 1787 atoms. Found 10 (13 requested) and removed 8 (6 requested) atoms. Cycle 9: After refmac, R = 0.1899 (Rfree = 0.000) for 1786 atoms. Found 2 (13 requested) and removed 7 (6 requested) atoms. Cycle 10: After refmac, R = 0.1925 (Rfree = 0.000) for 1778 atoms. Found 6 (13 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.92 3.04 Search for helices and strands: 0 residues in 0 chains, 1816 seeds are put forward Round 1: 131 peptides, 19 chains. Longest chain 15 peptides. Score 0.529 Round 2: 150 peptides, 20 chains. Longest chain 20 peptides. Score 0.602 Round 3: 134 peptides, 18 chains. Longest chain 20 peptides. Score 0.567 Round 4: 149 peptides, 16 chains. Longest chain 25 peptides. Score 0.676 Round 5: 145 peptides, 17 chains. Longest chain 25 peptides. Score 0.640 Taking the results from Round 4 Chains 18, Residues 133, Estimated correctness of the model 51.5 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 3446 reflections ( 98.15 % complete ) and 3828 restraints for refining 1803 atoms. 3271 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2018 (Rfree = 0.000) for 1803 atoms. Found 11 (13 requested) and removed 8 (6 requested) atoms. Cycle 12: After refmac, R = 0.1848 (Rfree = 0.000) for 1799 atoms. Found 8 (13 requested) and removed 6 (6 requested) atoms. Cycle 13: After refmac, R = 0.1762 (Rfree = 0.000) for 1799 atoms. Found 2 (13 requested) and removed 7 (6 requested) atoms. Cycle 14: After refmac, R = 0.1726 (Rfree = 0.000) for 1792 atoms. Found 5 (13 requested) and removed 10 (6 requested) atoms. Cycle 15: After refmac, R = 0.1685 (Rfree = 0.000) for 1785 atoms. Found 4 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.93 3.05 Search for helices and strands: 0 residues in 0 chains, 1834 seeds are put forward Round 1: 124 peptides, 19 chains. Longest chain 14 peptides. Score 0.490 Round 2: 133 peptides, 20 chains. Longest chain 14 peptides. Score 0.516 Round 3: 136 peptides, 20 chains. Longest chain 12 peptides. Score 0.532 Round 4: 139 peptides, 21 chains. Longest chain 14 peptides. Score 0.525 Round 5: 155 peptides, 25 chains. Longest chain 11 peptides. Score 0.518 Taking the results from Round 3 Chains 20, Residues 116, Estimated correctness of the model 4.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3446 reflections ( 98.15 % complete ) and 4149 restraints for refining 1804 atoms. 3705 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1926 (Rfree = 0.000) for 1804 atoms. Found 5 (13 requested) and removed 8 (6 requested) atoms. Cycle 17: After refmac, R = 0.1777 (Rfree = 0.000) for 1792 atoms. Found 7 (13 requested) and removed 7 (6 requested) atoms. Cycle 18: After refmac, R = 0.1814 (Rfree = 0.000) for 1787 atoms. Found 2 (13 requested) and removed 6 (6 requested) atoms. Cycle 19: After refmac, R = 0.1683 (Rfree = 0.000) for 1780 atoms. Found 5 (13 requested) and removed 6 (6 requested) atoms. Cycle 20: After refmac, R = 0.1611 (Rfree = 0.000) for 1774 atoms. Found 9 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.96 3.08 Search for helices and strands: 0 residues in 0 chains, 1823 seeds are put forward Round 1: 106 peptides, 21 chains. Longest chain 12 peptides. Score 0.325 Round 2: 113 peptides, 18 chains. Longest chain 13 peptides. Score 0.452 Round 3: 112 peptides, 15 chains. Longest chain 15 peptides. Score 0.522 Round 4: 120 peptides, 19 chains. Longest chain 18 peptides. Score 0.467 Round 5: 130 peptides, 19 chains. Longest chain 18 peptides. Score 0.523 Taking the results from Round 5 Chains 19, Residues 111, Estimated correctness of the model 1.5 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 3446 reflections ( 98.15 % complete ) and 4039 restraints for refining 1804 atoms. 3564 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1852 (Rfree = 0.000) for 1804 atoms. Found 7 (13 requested) and removed 6 (6 requested) atoms. Cycle 22: After refmac, R = 0.1709 (Rfree = 0.000) for 1798 atoms. Found 7 (13 requested) and removed 8 (6 requested) atoms. Cycle 23: After refmac, R = 0.1601 (Rfree = 0.000) for 1795 atoms. Found 4 (13 requested) and removed 6 (6 requested) atoms. Failed to save intermediate PDB Cycle 24: After refmac, R = 0.1533 (Rfree = 0.000) for 1792 atoms. Found 4 (13 requested) and removed 7 (6 requested) atoms. Cycle 25: After refmac, R = 0.1509 (Rfree = 0.000) for 1788 atoms. Found 3 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.00 3.12 Search for helices and strands: 0 residues in 0 chains, 1827 seeds are put forward Round 1: 97 peptides, 18 chains. Longest chain 13 peptides. Score 0.350 Round 2: 106 peptides, 16 chains. Longest chain 12 peptides. Score 0.462 Round 3: 113 peptides, 15 chains. Longest chain 19 peptides. Score 0.528 Round 4: 108 peptides, 19 chains. Longest chain 10 peptides. Score 0.394 Round 5: 112 peptides, 14 chains. Longest chain 19 peptides. Score 0.547 Taking the results from Round 5 Chains 14, Residues 98, Estimated correctness of the model 10.4 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 3446 reflections ( 98.15 % complete ) and 4212 restraints for refining 1804 atoms. 3818 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1882 (Rfree = 0.000) for 1804 atoms. Found 13 (13 requested) and removed 6 (6 requested) atoms. Cycle 27: After refmac, R = 0.1691 (Rfree = 0.000) for 1808 atoms. Found 8 (13 requested) and removed 7 (6 requested) atoms. Cycle 28: After refmac, R = 0.1611 (Rfree = 0.000) for 1806 atoms. Found 3 (13 requested) and removed 6 (6 requested) atoms. Cycle 29: After refmac, R = 0.1568 (Rfree = 0.000) for 1801 atoms. Found 3 (13 requested) and removed 6 (6 requested) atoms. Cycle 30: After refmac, R = 0.1556 (Rfree = 0.000) for 1796 atoms. Found 2 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.97 3.09 Search for helices and strands: 0 residues in 0 chains, 1832 seeds are put forward Round 1: 103 peptides, 21 chains. Longest chain 11 peptides. Score 0.305 Round 2: 113 peptides, 17 chains. Longest chain 17 peptides. Score 0.478 Round 3: 97 peptides, 16 chains. Longest chain 13 peptides. Score 0.407 Round 4: 111 peptides, 16 chains. Longest chain 17 peptides. Score 0.491 Round 5: 114 peptides, 16 chains. Longest chain 18 peptides. Score 0.509 Taking the results from Round 5 Chains 16, Residues 98, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3446 reflections ( 98.15 % complete ) and 4165 restraints for refining 1804 atoms. 3789 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1893 (Rfree = 0.000) for 1804 atoms. Found 6 (13 requested) and removed 6 (6 requested) atoms. Cycle 32: After refmac, R = 0.1725 (Rfree = 0.000) for 1803 atoms. Found 2 (13 requested) and removed 6 (6 requested) atoms. Cycle 33: After refmac, R = 0.1677 (Rfree = 0.000) for 1797 atoms. Found 7 (13 requested) and removed 6 (6 requested) atoms. Cycle 34: After refmac, R = 0.1609 (Rfree = 0.000) for 1797 atoms. Found 1 (13 requested) and removed 6 (6 requested) atoms. Cycle 35: After refmac, R = 0.1577 (Rfree = 0.000) for 1792 atoms. Found 2 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.00 3.12 Search for helices and strands: 0 residues in 0 chains, 1811 seeds are put forward Round 1: 97 peptides, 16 chains. Longest chain 9 peptides. Score 0.407 Round 2: 101 peptides, 17 chains. Longest chain 11 peptides. Score 0.404 Round 3: 94 peptides, 15 chains. Longest chain 12 peptides. Score 0.415 Round 4: 97 peptides, 15 chains. Longest chain 17 peptides. Score 0.434 Round 5: 106 peptides, 14 chains. Longest chain 19 peptides. Score 0.514 Taking the results from Round 5 Chains 14, Residues 92, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3446 reflections ( 98.15 % complete ) and 4123 restraints for refining 1804 atoms. 3769 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1807 (Rfree = 0.000) for 1804 atoms. Found 9 (13 requested) and removed 6 (6 requested) atoms. Cycle 37: After refmac, R = 0.1701 (Rfree = 0.000) for 1807 atoms. Found 3 (13 requested) and removed 6 (6 requested) atoms. Cycle 38: After refmac, R = 0.1702 (Rfree = 0.000) for 1802 atoms. Found 1 (13 requested) and removed 9 (6 requested) atoms. Cycle 39: After refmac, R = 0.1659 (Rfree = 0.000) for 1794 atoms. Found 6 (13 requested) and removed 7 (6 requested) atoms. Cycle 40: After refmac, R = 0.1628 (Rfree = 0.000) for 1793 atoms. Found 4 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.98 3.10 Search for helices and strands: 0 residues in 0 chains, 1832 seeds are put forward Round 1: 91 peptides, 19 chains. Longest chain 8 peptides. Score 0.279 Round 2: 100 peptides, 19 chains. Longest chain 10 peptides. Score 0.342 Round 3: 114 peptides, 18 chains. Longest chain 11 peptides. Score 0.458 Round 4: 113 peptides, 18 chains. Longest chain 13 peptides. Score 0.452 Round 5: 104 peptides, 16 chains. Longest chain 14 peptides. Score 0.450 Taking the results from Round 3 Chains 18, Residues 96, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3446 reflections ( 98.15 % complete ) and 4087 restraints for refining 1804 atoms. 3721 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1851 (Rfree = 0.000) for 1804 atoms. Found 6 (13 requested) and removed 6 (6 requested) atoms. Cycle 42: After refmac, R = 0.1731 (Rfree = 0.000) for 1803 atoms. Found 2 (13 requested) and removed 6 (6 requested) atoms. Cycle 43: After refmac, R = 0.1731 (Rfree = 0.000) for 1797 atoms. Found 3 (13 requested) and removed 6 (6 requested) atoms. Cycle 44: After refmac, R = 0.1755 (Rfree = 0.000) for 1794 atoms. Found 5 (13 requested) and removed 6 (6 requested) atoms. Cycle 45: After refmac, R = 0.1702 (Rfree = 0.000) for 1792 atoms. Found 5 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.02 3.14 Search for helices and strands: 0 residues in 0 chains, 1833 seeds are put forward Round 1: 74 peptides, 15 chains. Longest chain 9 peptides. Score 0.278 Round 2: 73 peptides, 12 chains. Longest chain 10 peptides. Score 0.364 Round 3: 75 peptides, 13 chains. Longest chain 9 peptides. Score 0.347 Round 4: 78 peptides, 14 chains. Longest chain 9 peptides. Score 0.338 Round 5: 84 peptides, 15 chains. Longest chain 10 peptides. Score 0.349 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 12, Residues 61, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2gjg-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3446 reflections ( 98.15 % complete ) and 4407 restraints for refining 1803 atoms. 4175 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1801 (Rfree = 0.000) for 1803 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.1778 (Rfree = 0.000) for 1797 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.1737 (Rfree = 0.000) for 1791 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.1758 (Rfree = 0.000) for 1785 atoms. TimeTaking 31.13