Sun 23 Dec 22:22:59 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 2oc5-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2oc5-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2oc5-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2oc5-3.4-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/2oc5-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2oc5-3.4-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 22:23:08 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/2oc5-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2oc5-3.4-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 239 and 0 Target number of residues in the AU: 239 Target solvent content: 0.6307 Checking the provided sequence file Detected sequence length: 244 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 244 Adjusted target solvent content: 0.62 Input MTZ file: 2oc5-3.4-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: 96 Cell parameters: 77.390 77.390 116.960 90.000 90.000 90.000 Input sequence file: 2oc5-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 1952 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: 29.240 3.400 Wilson plot Bfac: 66.60 5240 reflections ( 99.28 % complete ) and 0 restraints for refining 2152 atoms. Observations/parameters ratio is 0.61 ------------------------------------------------------ Starting model: R = 0.3223 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2261 (Rfree = 0.000) for 2152 atoms. Found 16 (16 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.25 2.76 Search for helices and strands: 0 residues in 0 chains, 2227 seeds are put forward Round 1: 136 peptides, 23 chains. Longest chain 14 peptides. Score 0.396 Round 2: 158 peptides, 20 chains. Longest chain 16 peptides. Score 0.546 Round 3: 169 peptides, 19 chains. Longest chain 22 peptides. Score 0.602 Round 4: 167 peptides, 21 chains. Longest chain 19 peptides. Score 0.562 Round 5: 161 peptides, 18 chains. Longest chain 25 peptides. Score 0.590 Taking the results from Round 3 Chains 20, Residues 150, Estimated correctness of the model 29.3 % 4 chains (64 residues) have been docked in sequence ------------------------------------------------------ 5240 reflections ( 99.28 % complete ) and 3249 restraints for refining 1815 atoms. 2394 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2588 (Rfree = 0.000) for 1815 atoms. Found 13 (13 requested) and removed 18 (6 requested) atoms. Cycle 2: After refmac, R = 0.2389 (Rfree = 0.000) for 1770 atoms. Found 12 (13 requested) and removed 8 (6 requested) atoms. Cycle 3: After refmac, R = 0.2299 (Rfree = 0.000) for 1748 atoms. Found 13 (13 requested) and removed 9 (6 requested) atoms. Cycle 4: After refmac, R = 0.2170 (Rfree = 0.000) for 1741 atoms. Found 10 (13 requested) and removed 10 (6 requested) atoms. Cycle 5: After refmac, R = 0.2103 (Rfree = 0.000) for 1735 atoms. Found 9 (13 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.26 2.77 Search for helices and strands: 0 residues in 0 chains, 1826 seeds are put forward Round 1: 171 peptides, 22 chains. Longest chain 18 peptides. Score 0.560 Round 2: 169 peptides, 22 chains. Longest chain 21 peptides. Score 0.553 Round 3: 179 peptides, 16 chains. Longest chain 32 peptides. Score 0.679 Round 4: 175 peptides, 17 chains. Longest chain 23 peptides. Score 0.653 Round 5: 167 peptides, 16 chains. Longest chain 30 peptides. Score 0.642 Taking the results from Round 3 Chains 20, Residues 163, Estimated correctness of the model 52.3 % 2 chains (42 residues) have been docked in sequence ------------------------------------------------------ 5240 reflections ( 99.28 % complete ) and 3276 restraints for refining 1773 atoms. 2462 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2592 (Rfree = 0.000) for 1773 atoms. Found 13 (13 requested) and removed 19 (6 requested) atoms. Cycle 7: After refmac, R = 0.2446 (Rfree = 0.000) for 1755 atoms. Found 8 (13 requested) and removed 11 (6 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.2360 (Rfree = 0.000) for 1748 atoms. Found 5 (13 requested) and removed 7 (6 requested) atoms. Cycle 9: After refmac, R = 0.2267 (Rfree = 0.000) for 1742 atoms. Found 6 (13 requested) and removed 6 (6 requested) atoms. Cycle 10: After refmac, R = 0.2226 (Rfree = 0.000) for 1740 atoms. Found 6 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.28 2.79 Search for helices and strands: 0 residues in 0 chains, 1805 seeds are put forward Round 1: 165 peptides, 18 chains. Longest chain 27 peptides. Score 0.604 Round 2: 175 peptides, 17 chains. Longest chain 29 peptides. Score 0.653 Round 3: 174 peptides, 23 chains. Longest chain 20 peptides. Score 0.555 Round 4: 178 peptides, 18 chains. Longest chain 29 peptides. Score 0.647 Round 5: 182 peptides, 24 chains. Longest chain 31 peptides. Score 0.568 Taking the results from Round 2 Chains 17, Residues 158, Estimated correctness of the model 45.0 % 3 chains (58 residues) have been docked in sequence ------------------------------------------------------ 5240 reflections ( 99.28 % complete ) and 3208 restraints for refining 1775 atoms. 2359 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2579 (Rfree = 0.000) for 1775 atoms. Found 13 (13 requested) and removed 18 (6 requested) atoms. Cycle 12: After refmac, R = 0.2317 (Rfree = 0.000) for 1759 atoms. Found 7 (13 requested) and removed 8 (6 requested) atoms. Cycle 13: After refmac, R = 0.2288 (Rfree = 0.000) for 1752 atoms. Found 9 (13 requested) and removed 13 (6 requested) atoms. Cycle 14: After refmac, R = 0.2202 (Rfree = 0.000) for 1746 atoms. Found 5 (13 requested) and removed 6 (6 requested) atoms. Cycle 15: After refmac, R = 0.2146 (Rfree = 0.000) for 1742 atoms. Found 6 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.30 2.80 Search for helices and strands: 0 residues in 0 chains, 1818 seeds are put forward Round 1: 160 peptides, 19 chains. Longest chain 18 peptides. Score 0.570 Round 2: 164 peptides, 18 chains. Longest chain 19 peptides. Score 0.601 Round 3: 171 peptides, 22 chains. Longest chain 19 peptides. Score 0.560 Round 4: 162 peptides, 19 chains. Longest chain 21 peptides. Score 0.578 Round 5: 170 peptides, 16 chains. Longest chain 42 peptides. Score 0.652 Taking the results from Round 5 Chains 18, Residues 154, Estimated correctness of the model 44.7 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 5240 reflections ( 99.28 % complete ) and 3784 restraints for refining 1775 atoms. 3137 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2511 (Rfree = 0.000) for 1775 atoms. Found 13 (13 requested) and removed 9 (6 requested) atoms. Cycle 17: After refmac, R = 0.2243 (Rfree = 0.000) for 1766 atoms. Found 6 (13 requested) and removed 6 (6 requested) atoms. Cycle 18: After refmac, R = 0.2129 (Rfree = 0.000) for 1762 atoms. Found 6 (13 requested) and removed 6 (6 requested) atoms. Cycle 19: After refmac, R = 0.2063 (Rfree = 0.000) for 1759 atoms. Found 4 (13 requested) and removed 6 (6 requested) atoms. Cycle 20: After refmac, R = 0.2108 (Rfree = 0.000) for 1753 atoms. Found 6 (13 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.30 2.80 Search for helices and strands: 0 residues in 0 chains, 1824 seeds are put forward Round 1: 156 peptides, 20 chains. Longest chain 16 peptides. Score 0.538 Round 2: 173 peptides, 21 chains. Longest chain 22 peptides. Score 0.584 Round 3: 169 peptides, 20 chains. Longest chain 19 peptides. Score 0.586 Round 4: 165 peptides, 19 chains. Longest chain 16 peptides. Score 0.588 Round 5: 170 peptides, 23 chains. Longest chain 18 peptides. Score 0.540 Taking the results from Round 4 Chains 19, Residues 146, Estimated correctness of the model 24.7 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 5240 reflections ( 99.28 % complete ) and 3725 restraints for refining 1775 atoms. 3098 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2435 (Rfree = 0.000) for 1775 atoms. Found 13 (13 requested) and removed 9 (6 requested) atoms. Cycle 22: After refmac, R = 0.2255 (Rfree = 0.000) for 1774 atoms. Found 13 (13 requested) and removed 7 (6 requested) atoms. Cycle 23: After refmac, R = 0.2155 (Rfree = 0.000) for 1776 atoms. Found 11 (13 requested) and removed 6 (6 requested) atoms. Cycle 24: After refmac, R = 0.2083 (Rfree = 0.000) for 1780 atoms. Found 4 (13 requested) and removed 7 (6 requested) atoms. Cycle 25: After refmac, R = 0.2058 (Rfree = 0.000) for 1776 atoms. Found 6 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.32 2.82 Search for helices and strands: 0 residues in 0 chains, 1831 seeds are put forward Round 1: 149 peptides, 21 chains. Longest chain 13 peptides. Score 0.492 Round 2: 149 peptides, 20 chains. Longest chain 14 peptides. Score 0.510 Round 3: 152 peptides, 22 chains. Longest chain 13 peptides. Score 0.486 Round 4: 152 peptides, 20 chains. Longest chain 16 peptides. Score 0.522 Round 5: 154 peptides, 17 chains. Longest chain 21 peptides. Score 0.582 Taking the results from Round 5 Chains 19, Residues 137, Estimated correctness of the model 22.7 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 5240 reflections ( 99.28 % complete ) and 3864 restraints for refining 1775 atoms. 3301 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2435 (Rfree = 0.000) for 1775 atoms. Found 13 (13 requested) and removed 11 (6 requested) atoms. Cycle 27: After refmac, R = 0.2211 (Rfree = 0.000) for 1769 atoms. Found 8 (13 requested) and removed 9 (6 requested) atoms. Cycle 28: After refmac, R = 0.2128 (Rfree = 0.000) for 1762 atoms. Found 8 (13 requested) and removed 7 (6 requested) atoms. Cycle 29: After refmac, R = 0.2078 (Rfree = 0.000) for 1761 atoms. Found 5 (13 requested) and removed 7 (6 requested) atoms. Cycle 30: After refmac, R = 0.2036 (Rfree = 0.000) for 1757 atoms. Found 2 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.28 2.79 Search for helices and strands: 0 residues in 0 chains, 1847 seeds are put forward Round 1: 142 peptides, 22 chains. Longest chain 13 peptides. Score 0.443 Round 2: 138 peptides, 19 chains. Longest chain 16 peptides. Score 0.484 Round 3: 147 peptides, 21 chains. Longest chain 18 peptides. Score 0.484 Round 4: 154 peptides, 20 chains. Longest chain 21 peptides. Score 0.530 Round 5: 148 peptides, 19 chains. Longest chain 21 peptides. Score 0.524 Taking the results from Round 4 Chains 22, Residues 134, Estimated correctness of the model 4.2 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 5240 reflections ( 99.28 % complete ) and 3810 restraints for refining 1775 atoms. 3249 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2323 (Rfree = 0.000) for 1775 atoms. Found 11 (13 requested) and removed 8 (6 requested) atoms. Cycle 32: After refmac, R = 0.2135 (Rfree = 0.000) for 1773 atoms. Found 3 (13 requested) and removed 7 (6 requested) atoms. Cycle 33: After refmac, R = 0.2079 (Rfree = 0.000) for 1768 atoms. Found 3 (13 requested) and removed 6 (6 requested) atoms. Cycle 34: After refmac, R = 0.2043 (Rfree = 0.000) for 1764 atoms. Found 8 (13 requested) and removed 6 (6 requested) atoms. Cycle 35: After refmac, R = 0.1969 (Rfree = 0.000) for 1765 atoms. Found 2 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.29 2.80 Search for helices and strands: 0 residues in 0 chains, 1839 seeds are put forward Round 1: 136 peptides, 23 chains. Longest chain 12 peptides. Score 0.396 Round 2: 156 peptides, 22 chains. Longest chain 13 peptides. Score 0.502 Round 3: 150 peptides, 18 chains. Longest chain 15 peptides. Score 0.550 Round 4: 148 peptides, 20 chains. Longest chain 17 peptides. Score 0.506 Round 5: 149 peptides, 20 chains. Longest chain 13 peptides. Score 0.510 Taking the results from Round 3 Chains 18, Residues 132, Estimated correctness of the model 11.5 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 5240 reflections ( 99.28 % complete ) and 3859 restraints for refining 1775 atoms. 3296 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2332 (Rfree = 0.000) for 1775 atoms. Found 11 (13 requested) and removed 10 (6 requested) atoms. Cycle 37: After refmac, R = 0.2104 (Rfree = 0.000) for 1770 atoms. Found 4 (13 requested) and removed 8 (6 requested) atoms. Cycle 38: After refmac, R = 0.2057 (Rfree = 0.000) for 1758 atoms. Found 6 (13 requested) and removed 6 (6 requested) atoms. Cycle 39: After refmac, R = 0.2030 (Rfree = 0.000) for 1755 atoms. Found 5 (13 requested) and removed 7 (6 requested) atoms. Cycle 40: After refmac, R = 0.1999 (Rfree = 0.000) for 1748 atoms. Found 6 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.25 2.76 Search for helices and strands: 0 residues in 0 chains, 1822 seeds are put forward Round 1: 132 peptides, 22 chains. Longest chain 11 peptides. Score 0.398 Round 2: 156 peptides, 21 chains. Longest chain 18 peptides. Score 0.520 Round 3: 164 peptides, 23 chains. Longest chain 12 peptides. Score 0.517 Round 4: 161 peptides, 21 chains. Longest chain 13 peptides. Score 0.540 Round 5: 161 peptides, 22 chains. Longest chain 17 peptides. Score 0.522 Taking the results from Round 4 Chains 21, Residues 140, Estimated correctness of the model 7.9 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 5240 reflections ( 99.28 % complete ) and 3862 restraints for refining 1775 atoms. 3289 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2332 (Rfree = 0.000) for 1775 atoms. Found 13 (13 requested) and removed 7 (6 requested) atoms. Cycle 42: After refmac, R = 0.2187 (Rfree = 0.000) for 1771 atoms. Found 13 (13 requested) and removed 7 (6 requested) atoms. Cycle 43: After refmac, R = 0.2165 (Rfree = 0.000) for 1776 atoms. Found 7 (13 requested) and removed 8 (6 requested) atoms. Cycle 44: After refmac, R = 0.2129 (Rfree = 0.000) for 1774 atoms. Found 11 (13 requested) and removed 7 (6 requested) atoms. Cycle 45: After refmac, R = 0.2099 (Rfree = 0.000) for 1777 atoms. Found 11 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.27 2.78 Search for helices and strands: 0 residues in 0 chains, 1868 seeds are put forward Round 1: 137 peptides, 21 chains. Longest chain 12 peptides. Score 0.441 Round 2: 149 peptides, 21 chains. Longest chain 13 peptides. Score 0.492 Round 3: 151 peptides, 25 chains. Longest chain 12 peptides. Score 0.425 Round 4: 160 peptides, 21 chains. Longest chain 20 peptides. Score 0.536 Round 5: 153 peptides, 21 chains. Longest chain 16 peptides. Score 0.508 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 21, Residues 139, Estimated correctness of the model 6.4 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2oc5-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5240 reflections ( 99.28 % complete ) and 4022 restraints for refining 1775 atoms. 3487 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2227 (Rfree = 0.000) for 1775 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.2097 (Rfree = 0.000) for 1766 atoms. Found 0 (13 requested) and removed 2 (6 requested) atoms. Cycle 48: After refmac, R = 0.2041 (Rfree = 0.000) for 1761 atoms. Found 0 (13 requested) and removed 0 (6 requested) atoms. Failed to save intermediate PDB Cycle 49: After refmac, R = 0.1996 (Rfree = 0.000) for 1760 atoms. Found 0 (13 requested) and removed 0 (6 requested) atoms. Writing output files ... TimeTaking 42.92