Sun 23 Dec 22:23:10 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 2a3n-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2a3n-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2a3n-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a3n-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/2a3n-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a3n-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 22:23:20 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/2a3n-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a3n-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 229 and 0 Target number of residues in the AU: 229 Target solvent content: 0.6394 Checking the provided sequence file Detected sequence length: 355 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 355 Adjusted target solvent content: 0.44 Input MTZ file: 2a3n-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: 81.220 102.610 49.296 90.000 123.209 90.000 Input sequence file: 2a3n-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 2840 target number of atoms Had to go as low as 0.75 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: 56.657 3.400 Wilson plot Bfac: 71.34 4686 reflections ( 99.81 % complete ) and 0 restraints for refining 3154 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Starting model: R = 0.3265 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2683 (Rfree = 0.000) for 3154 atoms. Found 12 (23 requested) and removed 20 (11 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.48 3.77 Search for helices and strands: 0 residues in 0 chains, 3225 seeds are put forward Round 1: 134 peptides, 27 chains. Longest chain 8 peptides. Score 0.306 Round 2: 172 peptides, 29 chains. Longest chain 21 peptides. Score 0.445 Round 3: 185 peptides, 24 chains. Longest chain 22 peptides. Score 0.584 Round 4: 196 peptides, 28 chains. Longest chain 14 peptides. Score 0.559 Round 5: 196 peptides, 23 chains. Longest chain 18 peptides. Score 0.636 Taking the results from Round 5 Chains 25, Residues 173, Estimated correctness of the model 40.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 4686 reflections ( 99.81 % complete ) and 5675 restraints for refining 2583 atoms. 4972 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2254 (Rfree = 0.000) for 2583 atoms. Found 10 (19 requested) and removed 16 (9 requested) atoms. Cycle 2: After refmac, R = 0.2041 (Rfree = 0.000) for 2551 atoms. Found 9 (19 requested) and removed 12 (9 requested) atoms. Cycle 3: After refmac, R = 0.1935 (Rfree = 0.000) for 2535 atoms. Found 6 (19 requested) and removed 12 (9 requested) atoms. Cycle 4: After refmac, R = 0.1914 (Rfree = 0.000) for 2526 atoms. Found 4 (19 requested) and removed 10 (9 requested) atoms. Cycle 5: After refmac, R = 0.1887 (Rfree = 0.000) for 2515 atoms. Found 3 (19 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.31 3.59 Search for helices and strands: 0 residues in 0 chains, 2643 seeds are put forward Round 1: 185 peptides, 33 chains. Longest chain 14 peptides. Score 0.427 Round 2: 189 peptides, 27 chains. Longest chain 16 peptides. Score 0.549 Round 3: 206 peptides, 28 chains. Longest chain 24 peptides. Score 0.595 Round 4: 190 peptides, 27 chains. Longest chain 17 peptides. Score 0.553 Round 5: 191 peptides, 26 chains. Longest chain 17 peptides. Score 0.573 Taking the results from Round 3 Chains 30, Residues 178, Estimated correctness of the model 27.0 % 3 chains (19 residues) have been docked in sequence ------------------------------------------------------ 4686 reflections ( 99.81 % complete ) and 5622 restraints for refining 2583 atoms. 4888 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2070 (Rfree = 0.000) for 2583 atoms. Found 12 (19 requested) and removed 14 (9 requested) atoms. Cycle 7: After refmac, R = 0.1997 (Rfree = 0.000) for 2572 atoms. Found 9 (19 requested) and removed 14 (9 requested) atoms. Cycle 8: After refmac, R = 0.2150 (Rfree = 0.000) for 2563 atoms. Found 16 (19 requested) and removed 11 (9 requested) atoms. Cycle 9: After refmac, R = 0.1773 (Rfree = 0.000) for 2561 atoms. Found 2 (19 requested) and removed 10 (9 requested) atoms. Cycle 10: After refmac, R = 0.1725 (Rfree = 0.000) for 2549 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.29 3.57 Search for helices and strands: 0 residues in 0 chains, 2653 seeds are put forward Round 1: 167 peptides, 28 chains. Longest chain 16 peptides. Score 0.442 Round 2: 188 peptides, 25 chains. Longest chain 19 peptides. Score 0.578 Round 3: 179 peptides, 24 chains. Longest chain 17 peptides. Score 0.562 Round 4: 184 peptides, 24 chains. Longest chain 24 peptides. Score 0.580 Round 5: 188 peptides, 26 chains. Longest chain 17 peptides. Score 0.562 Taking the results from Round 4 Chains 27, Residues 160, Estimated correctness of the model 22.0 % 4 chains (44 residues) have been docked in sequence ------------------------------------------------------ 4686 reflections ( 99.81 % complete ) and 5529 restraints for refining 2582 atoms. 4758 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2083 (Rfree = 0.000) for 2582 atoms. Found 16 (19 requested) and removed 16 (9 requested) atoms. Cycle 12: After refmac, R = 0.2106 (Rfree = 0.000) for 2575 atoms. Found 12 (19 requested) and removed 14 (9 requested) atoms. Cycle 13: After refmac, R = 0.1890 (Rfree = 0.000) for 2570 atoms. Found 6 (19 requested) and removed 16 (9 requested) atoms. Cycle 14: After refmac, R = 0.1940 (Rfree = 0.000) for 2554 atoms. Found 5 (19 requested) and removed 10 (9 requested) atoms. Cycle 15: After refmac, R = 0.2069 (Rfree = 0.000) for 2545 atoms. Found 18 (19 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.29 3.57 Search for helices and strands: 0 residues in 0 chains, 2625 seeds are put forward Round 1: 165 peptides, 28 chains. Longest chain 16 peptides. Score 0.433 Round 2: 176 peptides, 30 chains. Longest chain 14 peptides. Score 0.444 Round 3: 179 peptides, 27 chains. Longest chain 18 peptides. Score 0.511 Round 4: 181 peptides, 26 chains. Longest chain 18 peptides. Score 0.536 Round 5: 184 peptides, 25 chains. Longest chain 18 peptides. Score 0.564 Taking the results from Round 5 Chains 27, Residues 159, Estimated correctness of the model 16.5 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 4686 reflections ( 99.81 % complete ) and 5691 restraints for refining 2583 atoms. 5016 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2046 (Rfree = 0.000) for 2583 atoms. Found 17 (19 requested) and removed 11 (9 requested) atoms. Cycle 17: After refmac, R = 0.2003 (Rfree = 0.000) for 2581 atoms. Found 6 (19 requested) and removed 11 (9 requested) atoms. Cycle 18: After refmac, R = 0.1885 (Rfree = 0.000) for 2572 atoms. Found 7 (19 requested) and removed 12 (9 requested) atoms. Cycle 19: After refmac, R = 0.2041 (Rfree = 0.000) for 2564 atoms. Found 19 (19 requested) and removed 11 (9 requested) atoms. Cycle 20: After refmac, R = 0.1693 (Rfree = 0.000) for 2568 atoms. Found 8 (19 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.31 3.59 Search for helices and strands: 0 residues in 0 chains, 2692 seeds are put forward Round 1: 151 peptides, 28 chains. Longest chain 9 peptides. Score 0.369 Round 2: 163 peptides, 24 chains. Longest chain 13 peptides. Score 0.499 Round 3: 171 peptides, 25 chains. Longest chain 17 peptides. Score 0.514 Round 4: 169 peptides, 23 chains. Longest chain 24 peptides. Score 0.541 Round 5: 163 peptides, 22 chains. Longest chain 23 peptides. Score 0.535 Taking the results from Round 4 Chains 24, Residues 146, Estimated correctness of the model 8.3 % 2 chains (30 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 4686 reflections ( 99.81 % complete ) and 5630 restraints for refining 2583 atoms. 4957 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1841 (Rfree = 0.000) for 2583 atoms. Found 10 (19 requested) and removed 16 (9 requested) atoms. Cycle 22: After refmac, R = 0.1671 (Rfree = 0.000) for 2572 atoms. Found 6 (19 requested) and removed 10 (9 requested) atoms. Cycle 23: After refmac, R = 0.1700 (Rfree = 0.000) for 2565 atoms. Found 3 (19 requested) and removed 9 (9 requested) atoms. Cycle 24: After refmac, R = 0.1737 (Rfree = 0.000) for 2556 atoms. Found 9 (19 requested) and removed 11 (9 requested) atoms. Cycle 25: After refmac, R = 0.1588 (Rfree = 0.000) for 2551 atoms. Found 4 (19 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.32 3.60 Search for helices and strands: 0 residues in 0 chains, 2651 seeds are put forward Round 1: 156 peptides, 28 chains. Longest chain 12 peptides. Score 0.393 Round 2: 151 peptides, 25 chains. Longest chain 13 peptides. Score 0.429 Round 3: 150 peptides, 25 chains. Longest chain 13 peptides. Score 0.424 Round 4: 162 peptides, 27 chains. Longest chain 11 peptides. Score 0.439 Round 5: 150 peptides, 26 chains. Longest chain 9 peptides. Score 0.404 Taking the results from Round 4 Chains 27, Residues 135, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 4686 reflections ( 99.81 % complete ) and 6022 restraints for refining 2583 atoms. 5490 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1734 (Rfree = 0.000) for 2583 atoms. Found 8 (19 requested) and removed 10 (9 requested) atoms. Cycle 27: After refmac, R = 0.2009 (Rfree = 0.000) for 2570 atoms. Found 19 (19 requested) and removed 11 (9 requested) atoms. Cycle 28: After refmac, R = 0.1480 (Rfree = 0.000) for 2574 atoms. Found 5 (19 requested) and removed 9 (9 requested) atoms. Cycle 29: After refmac, R = 0.1494 (Rfree = 0.000) for 2566 atoms. Found 6 (19 requested) and removed 10 (9 requested) atoms. Cycle 30: After refmac, R = 0.1548 (Rfree = 0.000) for 2562 atoms. Found 12 (19 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.32 3.60 Search for helices and strands: 0 residues in 0 chains, 2668 seeds are put forward Round 1: 133 peptides, 27 chains. Longest chain 9 peptides. Score 0.301 Round 2: 156 peptides, 27 chains. Longest chain 14 peptides. Score 0.412 Round 3: 154 peptides, 25 chains. Longest chain 11 peptides. Score 0.442 Round 4: 145 peptides, 23 chains. Longest chain 16 peptides. Score 0.441 Round 5: 158 peptides, 25 chains. Longest chain 15 peptides. Score 0.459 Taking the results from Round 5 Chains 25, Residues 133, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4686 reflections ( 99.81 % complete ) and 6108 restraints for refining 2583 atoms. 5601 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1776 (Rfree = 0.000) for 2583 atoms. Found 9 (19 requested) and removed 9 (9 requested) atoms. Cycle 32: After refmac, R = 0.1626 (Rfree = 0.000) for 2574 atoms. Found 5 (19 requested) and removed 10 (9 requested) atoms. Cycle 33: After refmac, R = 0.1581 (Rfree = 0.000) for 2568 atoms. Found 0 (19 requested) and removed 11 (9 requested) atoms. Cycle 34: After refmac, R = 0.1604 (Rfree = 0.000) for 2556 atoms. Found 2 (19 requested) and removed 9 (9 requested) atoms. Cycle 35: After refmac, R = 0.1591 (Rfree = 0.000) for 2547 atoms. Found 4 (19 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.30 3.58 Search for helices and strands: 0 residues in 0 chains, 2627 seeds are put forward Round 1: 146 peptides, 29 chains. Longest chain 14 peptides. Score 0.324 Round 2: 150 peptides, 26 chains. Longest chain 14 peptides. Score 0.404 Round 3: 146 peptides, 26 chains. Longest chain 12 peptides. Score 0.386 Round 4: 159 peptides, 26 chains. Longest chain 16 peptides. Score 0.445 Round 5: 159 peptides, 25 chains. Longest chain 18 peptides. Score 0.464 Taking the results from Round 5 Chains 26, Residues 134, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4686 reflections ( 99.81 % complete ) and 5844 restraints for refining 2582 atoms. 5299 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1848 (Rfree = 0.000) for 2582 atoms. Found 10 (19 requested) and removed 10 (9 requested) atoms. Cycle 37: After refmac, R = 0.1753 (Rfree = 0.000) for 2577 atoms. Found 3 (19 requested) and removed 10 (9 requested) atoms. Cycle 38: After refmac, R = 0.1651 (Rfree = 0.000) for 2568 atoms. Found 4 (19 requested) and removed 9 (9 requested) atoms. Cycle 39: After refmac, R = 0.1642 (Rfree = 0.000) for 2562 atoms. Found 2 (19 requested) and removed 9 (9 requested) atoms. Cycle 40: After refmac, R = 0.1678 (Rfree = 0.000) for 2553 atoms. Found 5 (19 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.27 3.54 Search for helices and strands: 0 residues in 0 chains, 2634 seeds are put forward Round 1: 123 peptides, 25 chains. Longest chain 8 peptides. Score 0.293 Round 2: 139 peptides, 22 chains. Longest chain 15 peptides. Score 0.433 Round 3: 130 peptides, 21 chains. Longest chain 16 peptides. Score 0.412 Round 4: 125 peptides, 17 chains. Longest chain 16 peptides. Score 0.471 Round 5: 121 peptides, 20 chains. Longest chain 13 peptides. Score 0.390 Taking the results from Round 4 Chains 20, Residues 108, Estimated correctness of the model 0.0 % 3 chains (27 residues) have been docked in sequence ------------------------------------------------------ 4686 reflections ( 99.81 % complete ) and 5806 restraints for refining 2583 atoms. 5291 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1741 (Rfree = 0.000) for 2583 atoms. Found 11 (19 requested) and removed 10 (9 requested) atoms. Cycle 42: After refmac, R = 0.1608 (Rfree = 0.000) for 2581 atoms. Found 4 (19 requested) and removed 9 (9 requested) atoms. Cycle 43: After refmac, R = 0.1583 (Rfree = 0.000) for 2576 atoms. Found 2 (19 requested) and removed 9 (9 requested) atoms. Cycle 44: After refmac, R = 0.1594 (Rfree = 0.000) for 2569 atoms. Found 3 (19 requested) and removed 9 (9 requested) atoms. Cycle 45: After refmac, R = 0.1887 (Rfree = 0.000) for 2563 atoms. Found 19 (19 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.31 3.59 Search for helices and strands: 0 residues in 0 chains, 2656 seeds are put forward Round 1: 114 peptides, 24 chains. Longest chain 9 peptides. Score 0.268 Round 2: 138 peptides, 24 chains. Longest chain 13 peptides. Score 0.388 Round 3: 135 peptides, 22 chains. Longest chain 14 peptides. Score 0.415 Round 4: 149 peptides, 25 chains. Longest chain 14 peptides. Score 0.419 Round 5: 142 peptides, 25 chains. Longest chain 14 peptides. Score 0.387 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 25, Residues 124, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence Sequence coverage is 6 % Consider running further cycles of model building using 2a3n-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4686 reflections ( 99.81 % complete ) and 5932 restraints for refining 2583 atoms. 5430 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1686 (Rfree = 0.000) for 2583 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.2166 (Rfree = 0.000) for 2569 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 48: After refmac, R = 0.1894 (Rfree = 0.000) for 2555 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.1726 (Rfree = 0.000) for 2544 atoms. TimeTaking 49.08