Sun 23 Dec 22:22:52 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 2oc5-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2oc5-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2oc5-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2oc5-3.2-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/2oc5-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2oc5-3.2-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 22:23:00 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/2oc5-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2oc5-3.2-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 245 and 0 Target number of residues in the AU: 245 Target solvent content: 0.6214 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: 2oc5-3.2-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: 2oc5-3.2-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 3.200 Wilson plot Bfac: 62.01 6243 reflections ( 99.36 % complete ) and 0 restraints for refining 2152 atoms. Observations/parameters ratio is 0.73 ------------------------------------------------------ Starting model: R = 0.3241 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2731 (Rfree = 0.000) for 2152 atoms. Found 19 (19 requested) and removed 13 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.22 2.74 Search for helices and strands: 0 residues in 0 chains, 2209 seeds are put forward Round 1: 135 peptides, 22 chains. Longest chain 13 peptides. Score 0.412 Round 2: 170 peptides, 22 chains. Longest chain 20 peptides. Score 0.557 Round 3: 175 peptides, 21 chains. Longest chain 21 peptides. Score 0.591 Round 4: 176 peptides, 18 chains. Longest chain 20 peptides. Score 0.641 Round 5: 178 peptides, 20 chains. Longest chain 22 peptides. Score 0.617 Taking the results from Round 4 Chains 21, Residues 158, Estimated correctness of the model 51.6 % 4 chains (45 residues) have been docked in sequence ------------------------------------------------------ 6243 reflections ( 99.36 % complete ) and 3307 restraints for refining 1779 atoms. 2512 conditional restraints added. Observations/parameters ratio is 0.88 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2834 (Rfree = 0.000) for 1779 atoms. Found 15 (15 requested) and removed 17 (7 requested) atoms. Cycle 2: After refmac, R = 0.2722 (Rfree = 0.000) for 1748 atoms. Found 15 (15 requested) and removed 16 (7 requested) atoms. Cycle 3: After refmac, R = 0.2575 (Rfree = 0.000) for 1731 atoms. Found 15 (15 requested) and removed 13 (7 requested) atoms. Cycle 4: After refmac, R = 0.2540 (Rfree = 0.000) for 1722 atoms. Found 12 (15 requested) and removed 16 (7 requested) atoms. Cycle 5: After refmac, R = 0.2325 (Rfree = 0.000) for 1712 atoms. Found 4 (15 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.12 2.65 Search for helices and strands: 0 residues in 0 chains, 1780 seeds are put forward Round 1: 169 peptides, 21 chains. Longest chain 18 peptides. Score 0.570 Round 2: 176 peptides, 15 chains. Longest chain 26 peptides. Score 0.684 Round 3: 178 peptides, 17 chains. Longest chain 29 peptides. Score 0.662 Round 4: 179 peptides, 19 chains. Longest chain 31 peptides. Score 0.635 Round 5: 187 peptides, 19 chains. Longest chain 29 peptides. Score 0.660 Taking the results from Round 2 Chains 16, Residues 161, Estimated correctness of the model 61.7 % 3 chains (57 residues) have been docked in sequence ------------------------------------------------------ 6243 reflections ( 99.36 % complete ) and 3193 restraints for refining 1782 atoms. 2347 conditional restraints added. Observations/parameters ratio is 0.88 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2546 (Rfree = 0.000) for 1782 atoms. Found 15 (15 requested) and removed 14 (7 requested) atoms. Cycle 7: After refmac, R = 0.2326 (Rfree = 0.000) for 1769 atoms. Found 11 (16 requested) and removed 13 (8 requested) atoms. Cycle 8: After refmac, R = 0.2213 (Rfree = 0.000) for 1760 atoms. Found 6 (15 requested) and removed 10 (7 requested) atoms. Cycle 9: After refmac, R = 0.2235 (Rfree = 0.000) for 1748 atoms. Found 8 (15 requested) and removed 12 (7 requested) atoms. Cycle 10: After refmac, R = 0.2166 (Rfree = 0.000) for 1739 atoms. Found 5 (15 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.10 2.63 Search for helices and strands: 0 residues in 0 chains, 1808 seeds are put forward Round 1: 170 peptides, 18 chains. Longest chain 37 peptides. Score 0.621 Round 2: 179 peptides, 15 chains. Longest chain 33 peptides. Score 0.693 Round 3: 183 peptides, 22 chains. Longest chain 20 peptides. Score 0.603 Round 4: 176 peptides, 18 chains. Longest chain 21 peptides. Score 0.641 Round 5: 183 peptides, 19 chains. Longest chain 24 peptides. Score 0.648 Taking the results from Round 2 Chains 16, Residues 164, Estimated correctness of the model 63.7 % 4 chains (76 residues) have been docked in sequence ------------------------------------------------------ 6243 reflections ( 99.36 % complete ) and 2980 restraints for refining 1782 atoms. 2047 conditional restraints added. Observations/parameters ratio is 0.88 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2566 (Rfree = 0.000) for 1782 atoms. Found 15 (15 requested) and removed 17 (7 requested) atoms. Cycle 12: After refmac, R = 0.2338 (Rfree = 0.000) for 1771 atoms. Found 8 (15 requested) and removed 13 (7 requested) atoms. Cycle 13: After refmac, R = 0.2210 (Rfree = 0.000) for 1756 atoms. Found 7 (15 requested) and removed 11 (7 requested) atoms. Cycle 14: After refmac, R = 0.2167 (Rfree = 0.000) for 1745 atoms. Found 11 (15 requested) and removed 8 (7 requested) atoms. Cycle 15: After refmac, R = 0.2108 (Rfree = 0.000) for 1737 atoms. Found 6 (15 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.13 2.66 Search for helices and strands: 0 residues in 0 chains, 1805 seeds are put forward Round 1: 167 peptides, 17 chains. Longest chain 23 peptides. Score 0.627 Round 2: 190 peptides, 14 chains. Longest chain 37 peptides. Score 0.735 Round 3: 176 peptides, 17 chains. Longest chain 22 peptides. Score 0.656 Round 4: 175 peptides, 16 chains. Longest chain 26 peptides. Score 0.667 Round 5: 177 peptides, 18 chains. Longest chain 23 peptides. Score 0.644 Taking the results from Round 2 Chains 15, Residues 176, Estimated correctness of the model 72.3 % 2 chains (55 residues) have been docked in sequence Building loops using Loopy2018 15 chains (176 residues) following loop building 2 chains (55 residues) in sequence following loop building ------------------------------------------------------ 6243 reflections ( 99.36 % complete ) and 3060 restraints for refining 1782 atoms. 2164 conditional restraints added. Observations/parameters ratio is 0.88 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2442 (Rfree = 0.000) for 1782 atoms. Found 15 (15 requested) and removed 12 (7 requested) atoms. Cycle 17: After refmac, R = 0.2212 (Rfree = 0.000) for 1781 atoms. Found 10 (16 requested) and removed 11 (8 requested) atoms. Cycle 18: After refmac, R = 0.2366 (Rfree = 0.000) for 1771 atoms. Found 14 (14 requested) and removed 12 (7 requested) atoms. Cycle 19: After refmac, R = 0.2069 (Rfree = 0.000) for 1766 atoms. Found 8 (14 requested) and removed 7 (7 requested) atoms. Cycle 20: After refmac, R = 0.2004 (Rfree = 0.000) for 1762 atoms. Found 2 (14 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.20 2.72 Search for helices and strands: 0 residues in 0 chains, 1830 seeds are put forward Round 1: 157 peptides, 19 chains. Longest chain 22 peptides. Score 0.559 Round 2: 177 peptides, 17 chains. Longest chain 33 peptides. Score 0.659 Round 3: 169 peptides, 15 chains. Longest chain 34 peptides. Score 0.664 Round 4: 173 peptides, 17 chains. Longest chain 21 peptides. Score 0.646 Round 5: 164 peptides, 18 chains. Longest chain 28 peptides. Score 0.601 Taking the results from Round 3 Chains 15, Residues 154, Estimated correctness of the model 57.2 % 2 chains (53 residues) have been docked in sequence ------------------------------------------------------ 6243 reflections ( 99.36 % complete ) and 3316 restraints for refining 1782 atoms. 2515 conditional restraints added. Observations/parameters ratio is 0.88 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2418 (Rfree = 0.000) for 1782 atoms. Found 13 (13 requested) and removed 10 (7 requested) atoms. Cycle 22: After refmac, R = 0.2220 (Rfree = 0.000) for 1778 atoms. Found 9 (14 requested) and removed 10 (8 requested) atoms. Cycle 23: After refmac, R = 0.2128 (Rfree = 0.000) for 1773 atoms. Found 7 (13 requested) and removed 8 (7 requested) atoms. Cycle 24: After refmac, R = 0.2111 (Rfree = 0.000) for 1769 atoms. Found 9 (13 requested) and removed 8 (7 requested) atoms. Cycle 25: After refmac, R = 0.2005 (Rfree = 0.000) for 1769 atoms. Found 4 (13 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.15 2.68 Search for helices and strands: 0 residues in 0 chains, 1852 seeds are put forward Round 1: 162 peptides, 19 chains. Longest chain 23 peptides. Score 0.578 Round 2: 170 peptides, 14 chains. Longest chain 23 peptides. Score 0.681 Round 3: 158 peptides, 19 chains. Longest chain 16 peptides. Score 0.563 Round 4: 162 peptides, 17 chains. Longest chain 23 peptides. Score 0.610 Round 5: 158 peptides, 16 chains. Longest chain 25 peptides. Score 0.613 Taking the results from Round 2 Chains 15, Residues 156, Estimated correctness of the model 61.0 % 2 chains (37 residues) have been docked in sequence ------------------------------------------------------ 6243 reflections ( 99.36 % complete ) and 3479 restraints for refining 1782 atoms. 2720 conditional restraints added. Observations/parameters ratio is 0.88 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2445 (Rfree = 0.000) for 1782 atoms. Found 13 (13 requested) and removed 9 (7 requested) atoms. Cycle 27: After refmac, R = 0.2298 (Rfree = 0.000) for 1779 atoms. Found 12 (14 requested) and removed 15 (8 requested) atoms. Cycle 28: After refmac, R = 0.2428 (Rfree = 0.000) for 1770 atoms. Found 13 (13 requested) and removed 14 (7 requested) atoms. Cycle 29: After refmac, R = 0.2642 (Rfree = 0.000) for 1767 atoms. Found 13 (13 requested) and removed 14 (7 requested) atoms. Cycle 30: After refmac, R = 0.2513 (Rfree = 0.000) for 1758 atoms. Found 13 (13 requested) and removed 14 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.14 2.67 Search for helices and strands: 0 residues in 0 chains, 1830 seeds are put forward Round 1: 158 peptides, 19 chains. Longest chain 24 peptides. Score 0.563 Round 2: 177 peptides, 19 chains. Longest chain 23 peptides. Score 0.629 Round 3: 171 peptides, 19 chains. Longest chain 40 peptides. Score 0.609 Round 4: 165 peptides, 15 chains. Longest chain 45 peptides. Score 0.651 Round 5: 174 peptides, 19 chains. Longest chain 31 peptides. Score 0.619 Taking the results from Round 4 Chains 15, Residues 150, Estimated correctness of the model 54.1 % 2 chains (49 residues) have been docked in sequence ------------------------------------------------------ 6243 reflections ( 99.36 % complete ) and 3277 restraints for refining 1782 atoms. 2493 conditional restraints added. Observations/parameters ratio is 0.88 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2609 (Rfree = 0.000) for 1782 atoms. Found 13 (13 requested) and removed 22 (7 requested) atoms. Cycle 32: After refmac, R = 0.2432 (Rfree = 0.000) for 1770 atoms. Found 13 (13 requested) and removed 13 (7 requested) atoms. Cycle 33: After refmac, R = 0.2346 (Rfree = 0.000) for 1767 atoms. Found 10 (13 requested) and removed 11 (7 requested) atoms. Cycle 34: After refmac, R = 0.2302 (Rfree = 0.000) for 1763 atoms. Found 7 (13 requested) and removed 11 (7 requested) atoms. Cycle 35: After refmac, R = 0.2263 (Rfree = 0.000) for 1757 atoms. Found 2 (13 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.13 2.66 Search for helices and strands: 0 residues in 0 chains, 1835 seeds are put forward Round 1: 138 peptides, 17 chains. Longest chain 21 peptides. Score 0.521 Round 2: 148 peptides, 20 chains. Longest chain 13 peptides. Score 0.506 Round 3: 156 peptides, 17 chains. Longest chain 28 peptides. Score 0.589 Round 4: 158 peptides, 18 chains. Longest chain 17 peptides. Score 0.580 Round 5: 167 peptides, 21 chains. Longest chain 16 peptides. Score 0.562 Taking the results from Round 3 Chains 17, Residues 139, Estimated correctness of the model 38.1 % 1 chains (27 residues) have been docked in sequence ------------------------------------------------------ 6243 reflections ( 99.36 % complete ) and 3549 restraints for refining 1780 atoms. 2886 conditional restraints added. Observations/parameters ratio is 0.88 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2480 (Rfree = 0.000) for 1780 atoms. Found 12 (13 requested) and removed 14 (7 requested) atoms. Cycle 37: After refmac, R = 0.2513 (Rfree = 0.000) for 1774 atoms. Found 13 (13 requested) and removed 9 (7 requested) atoms. Cycle 38: After refmac, R = 0.2227 (Rfree = 0.000) for 1776 atoms. Found 3 (13 requested) and removed 9 (7 requested) atoms. Cycle 39: After refmac, R = 0.2226 (Rfree = 0.000) for 1766 atoms. Found 9 (13 requested) and removed 10 (7 requested) atoms. Cycle 40: After refmac, R = 0.2254 (Rfree = 0.000) for 1762 atoms. Found 13 (13 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.11 2.64 Search for helices and strands: 0 residues in 0 chains, 1838 seeds are put forward Round 1: 148 peptides, 22 chains. Longest chain 12 peptides. Score 0.469 Round 2: 151 peptides, 20 chains. Longest chain 13 peptides. Score 0.518 Round 3: 167 peptides, 19 chains. Longest chain 24 peptides. Score 0.595 Round 4: 167 peptides, 21 chains. Longest chain 16 peptides. Score 0.562 Round 5: 161 peptides, 22 chains. Longest chain 19 peptides. Score 0.522 Taking the results from Round 3 Chains 20, Residues 148, Estimated correctness of the model 39.7 % 3 chains (51 residues) have been docked in sequence ------------------------------------------------------ 6243 reflections ( 99.36 % complete ) and 3247 restraints for refining 1782 atoms. 2480 conditional restraints added. Observations/parameters ratio is 0.88 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2539 (Rfree = 0.000) for 1782 atoms. Found 13 (13 requested) and removed 20 (7 requested) atoms. Cycle 42: After refmac, R = 0.2420 (Rfree = 0.000) for 1763 atoms. Found 10 (13 requested) and removed 11 (7 requested) atoms. Cycle 43: After refmac, R = 0.2364 (Rfree = 0.000) for 1757 atoms. Found 13 (13 requested) and removed 10 (7 requested) atoms. Cycle 44: After refmac, R = 0.2199 (Rfree = 0.000) for 1753 atoms. Found 8 (13 requested) and removed 7 (7 requested) atoms. Cycle 45: After refmac, R = 0.2265 (Rfree = 0.000) for 1748 atoms. Found 12 (13 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.15 2.68 Search for helices and strands: 0 residues in 0 chains, 1829 seeds are put forward Round 1: 150 peptides, 21 chains. Longest chain 20 peptides. Score 0.496 Round 2: 147 peptides, 18 chains. Longest chain 18 peptides. Score 0.538 Round 3: 157 peptides, 15 chains. Longest chain 27 peptides. Score 0.625 Round 4: 164 peptides, 16 chains. Longest chain 23 peptides. Score 0.633 Round 5: 159 peptides, 18 chains. Longest chain 23 peptides. Score 0.583 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 16, Residues 148, Estimated correctness of the model 49.7 % 1 chains (21 residues) have been docked in sequence Sequence coverage is 14 % Consider running further cycles of model building using 2oc5-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6243 reflections ( 99.36 % complete ) and 3561 restraints for refining 1782 atoms. 2907 conditional restraints added. Observations/parameters ratio is 0.88 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2546 (Rfree = 0.000) for 1782 atoms. Found 0 (13 requested) and removed 5 (7 requested) atoms. Cycle 47: After refmac, R = 0.2335 (Rfree = 0.000) for 1775 atoms. Found 0 (13 requested) and removed 3 (7 requested) atoms. Cycle 48: After refmac, R = 0.2301 (Rfree = 0.000) for 1771 atoms. Found 0 (13 requested) and removed 2 (7 requested) atoms. Cycle 49: After refmac, R = 0.2289 (Rfree = 0.000) for 1768 atoms. TimeTaking 43.35