Sun 23 Dec 22:23:07 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 2ou6-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ou6-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ou6-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ou6-3.2-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/2ou6-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ou6-3.2-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 22:23:17 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/2ou6-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ou6-3.2-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 177 and 0 Target number of residues in the AU: 177 Target solvent content: 0.6057 Checking the provided sequence file Detected sequence length: 190 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 190 Adjusted target solvent content: 0.58 Input MTZ file: 2ou6-3.2-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: 179 Cell parameters: 57.933 57.933 250.773 90.000 90.000 120.000 Input sequence file: 2ou6-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 1520 target number of atoms Had to go as low as 0.80 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: 50.171 3.201 Wilson plot Bfac: 54.53 4637 reflections ( 99.83 % complete ) and 0 restraints for refining 1676 atoms. Observations/parameters ratio is 0.69 ------------------------------------------------------ Starting model: R = 0.3465 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3275 (Rfree = 0.000) for 1676 atoms. Found 15 (15 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.06 2.75 Search for helices and strands: 0 residues in 0 chains, 1720 seeds are put forward Round 1: 112 peptides, 19 chains. Longest chain 16 peptides. Score 0.426 Round 2: 111 peptides, 13 chains. Longest chain 25 peptides. Score 0.575 Round 3: 119 peptides, 14 chains. Longest chain 19 peptides. Score 0.592 Round 4: 121 peptides, 14 chains. Longest chain 16 peptides. Score 0.602 Round 5: 133 peptides, 18 chains. Longest chain 20 peptides. Score 0.572 Taking the results from Round 4 Chains 15, Residues 107, Estimated correctness of the model 41.5 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 4637 reflections ( 99.83 % complete ) and 2891 restraints for refining 1386 atoms. 2406 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3003 (Rfree = 0.000) for 1386 atoms. Found 12 (12 requested) and removed 16 (6 requested) atoms. Cycle 2: After refmac, R = 0.2890 (Rfree = 0.000) for 1360 atoms. Found 7 (12 requested) and removed 9 (6 requested) atoms. Cycle 3: After refmac, R = 0.2812 (Rfree = 0.000) for 1348 atoms. Found 10 (12 requested) and removed 8 (6 requested) atoms. Cycle 4: After refmac, R = 0.2666 (Rfree = 0.000) for 1348 atoms. Found 10 (12 requested) and removed 7 (6 requested) atoms. Cycle 5: After refmac, R = 0.2623 (Rfree = 0.000) for 1347 atoms. Found 6 (12 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.97 2.67 Search for helices and strands: 0 residues in 0 chains, 1412 seeds are put forward Round 1: 113 peptides, 17 chains. Longest chain 15 peptides. Score 0.485 Round 2: 123 peptides, 17 chains. Longest chain 14 peptides. Score 0.542 Round 3: 132 peptides, 16 chains. Longest chain 17 peptides. Score 0.611 Round 4: 130 peptides, 16 chains. Longest chain 16 peptides. Score 0.602 Round 5: 126 peptides, 15 chains. Longest chain 19 peptides. Score 0.604 Taking the results from Round 3 Chains 17, Residues 116, Estimated correctness of the model 43.9 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 4637 reflections ( 99.83 % complete ) and 2824 restraints for refining 1387 atoms. 2342 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2977 (Rfree = 0.000) for 1387 atoms. Found 11 (12 requested) and removed 6 (6 requested) atoms. Cycle 7: After refmac, R = 0.2859 (Rfree = 0.000) for 1385 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 8: After refmac, R = 0.2712 (Rfree = 0.000) for 1386 atoms. Found 8 (12 requested) and removed 6 (6 requested) atoms. Cycle 9: After refmac, R = 0.2688 (Rfree = 0.000) for 1386 atoms. Found 6 (12 requested) and removed 6 (6 requested) atoms. Cycle 10: After refmac, R = 0.2733 (Rfree = 0.000) for 1385 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.02 2.71 Search for helices and strands: 0 residues in 0 chains, 1448 seeds are put forward Round 1: 117 peptides, 17 chains. Longest chain 13 peptides. Score 0.509 Round 2: 126 peptides, 13 chains. Longest chain 22 peptides. Score 0.648 Round 3: 131 peptides, 15 chains. Longest chain 19 peptides. Score 0.628 Round 4: 130 peptides, 18 chains. Longest chain 13 peptides. Score 0.556 Round 5: 124 peptides, 16 chains. Longest chain 17 peptides. Score 0.571 Taking the results from Round 2 Chains 16, Residues 113, Estimated correctness of the model 53.3 % 2 chains (22 residues) have been docked in sequence ------------------------------------------------------ 4637 reflections ( 99.83 % complete ) and 2780 restraints for refining 1387 atoms. 2251 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2945 (Rfree = 0.000) for 1387 atoms. Found 9 (12 requested) and removed 17 (6 requested) atoms. Cycle 12: After refmac, R = 0.2829 (Rfree = 0.000) for 1371 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 13: After refmac, R = 0.2743 (Rfree = 0.000) for 1369 atoms. Found 11 (12 requested) and removed 6 (6 requested) atoms. Cycle 14: After refmac, R = 0.2671 (Rfree = 0.000) for 1370 atoms. Found 9 (12 requested) and removed 8 (6 requested) atoms. Cycle 15: After refmac, R = 0.2687 (Rfree = 0.000) for 1370 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.99 2.69 Search for helices and strands: 0 residues in 0 chains, 1431 seeds are put forward Round 1: 124 peptides, 20 chains. Longest chain 14 peptides. Score 0.473 Round 2: 124 peptides, 17 chains. Longest chain 14 peptides. Score 0.548 Round 3: 136 peptides, 19 chains. Longest chain 20 peptides. Score 0.564 Round 4: 138 peptides, 17 chains. Longest chain 23 peptides. Score 0.618 Round 5: 136 peptides, 14 chains. Longest chain 16 peptides. Score 0.671 Taking the results from Round 5 Chains 14, Residues 122, Estimated correctness of the model 58.7 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 4637 reflections ( 99.83 % complete ) and 2818 restraints for refining 1386 atoms. 2298 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2944 (Rfree = 0.000) for 1386 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 17: After refmac, R = 0.2840 (Rfree = 0.000) for 1384 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 18: After refmac, R = 0.2740 (Rfree = 0.000) for 1385 atoms. Found 11 (12 requested) and removed 7 (6 requested) atoms. Cycle 19: After refmac, R = 0.2763 (Rfree = 0.000) for 1385 atoms. Found 12 (12 requested) and removed 6 (6 requested) atoms. Cycle 20: After refmac, R = 0.2673 (Rfree = 0.000) for 1390 atoms. Found 11 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.01 2.70 Search for helices and strands: 0 residues in 0 chains, 1473 seeds are put forward Round 1: 113 peptides, 16 chains. Longest chain 13 peptides. Score 0.511 Round 2: 131 peptides, 18 chains. Longest chain 14 peptides. Score 0.561 Round 3: 135 peptides, 15 chains. Longest chain 21 peptides. Score 0.646 Round 4: 135 peptides, 19 chains. Longest chain 16 peptides. Score 0.559 Round 5: 143 peptides, 17 chains. Longest chain 18 peptides. Score 0.641 Taking the results from Round 3 Chains 17, Residues 120, Estimated correctness of the model 52.8 % 1 chains (16 residues) have been docked in sequence ------------------------------------------------------ 4637 reflections ( 99.83 % complete ) and 2763 restraints for refining 1387 atoms. 2232 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2905 (Rfree = 0.000) for 1387 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 22: After refmac, R = 0.2762 (Rfree = 0.000) for 1387 atoms. Found 11 (12 requested) and removed 8 (6 requested) atoms. Cycle 23: After refmac, R = 0.2758 (Rfree = 0.000) for 1389 atoms. Found 7 (12 requested) and removed 6 (6 requested) atoms. Cycle 24: After refmac, R = 0.2758 (Rfree = 0.000) for 1390 atoms. Found 5 (12 requested) and removed 7 (6 requested) atoms. Cycle 25: After refmac, R = 0.2655 (Rfree = 0.000) for 1388 atoms. Found 1 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.09 2.78 Search for helices and strands: 0 residues in 0 chains, 1454 seeds are put forward Round 1: 106 peptides, 18 chains. Longest chain 11 peptides. Score 0.415 Round 2: 131 peptides, 20 chains. Longest chain 13 peptides. Score 0.514 Round 3: 131 peptides, 18 chains. Longest chain 17 peptides. Score 0.561 Round 4: 123 peptides, 16 chains. Longest chain 18 peptides. Score 0.566 Round 5: 114 peptides, 15 chains. Longest chain 14 peptides. Score 0.542 Taking the results from Round 4 Chains 18, Residues 107, Estimated correctness of the model 31.5 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 4637 reflections ( 99.83 % complete ) and 2888 restraints for refining 1387 atoms. 2434 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3001 (Rfree = 0.000) for 1387 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. Cycle 27: After refmac, R = 0.2939 (Rfree = 0.000) for 1388 atoms. Found 7 (12 requested) and removed 6 (6 requested) atoms. Cycle 28: After refmac, R = 0.2771 (Rfree = 0.000) for 1387 atoms. Found 3 (12 requested) and removed 6 (6 requested) atoms. Cycle 29: After refmac, R = 0.2761 (Rfree = 0.000) for 1383 atoms. Found 2 (12 requested) and removed 6 (6 requested) atoms. Cycle 30: After refmac, R = 0.2733 (Rfree = 0.000) for 1376 atoms. Found 6 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.00 2.69 Search for helices and strands: 0 residues in 0 chains, 1435 seeds are put forward Round 1: 100 peptides, 17 chains. Longest chain 17 peptides. Score 0.404 Round 2: 113 peptides, 16 chains. Longest chain 17 peptides. Score 0.511 Round 3: 108 peptides, 15 chains. Longest chain 19 peptides. Score 0.508 Round 4: 113 peptides, 17 chains. Longest chain 14 peptides. Score 0.485 Round 5: 117 peptides, 16 chains. Longest chain 14 peptides. Score 0.534 Taking the results from Round 5 Chains 16, Residues 101, Estimated correctness of the model 22.0 % 3 chains (22 residues) have been docked in sequence ------------------------------------------------------ 4637 reflections ( 99.83 % complete ) and 2696 restraints for refining 1387 atoms. 2223 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2988 (Rfree = 0.000) for 1387 atoms. Found 11 (12 requested) and removed 9 (6 requested) atoms. Cycle 32: After refmac, R = 0.2802 (Rfree = 0.000) for 1374 atoms. Found 7 (12 requested) and removed 8 (6 requested) atoms. Cycle 33: After refmac, R = 0.2783 (Rfree = 0.000) for 1368 atoms. Found 7 (12 requested) and removed 6 (6 requested) atoms. Cycle 34: After refmac, R = 0.2729 (Rfree = 0.000) for 1368 atoms. Found 7 (12 requested) and removed 6 (6 requested) atoms. Cycle 35: After refmac, R = 0.2731 (Rfree = 0.000) for 1364 atoms. Found 8 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.97 2.67 Search for helices and strands: 0 residues in 0 chains, 1417 seeds are put forward Round 1: 104 peptides, 21 chains. Longest chain 8 peptides. Score 0.316 Round 2: 113 peptides, 17 chains. Longest chain 13 peptides. Score 0.485 Round 3: 99 peptides, 17 chains. Longest chain 12 peptides. Score 0.397 Round 4: 99 peptides, 16 chains. Longest chain 11 peptides. Score 0.426 Round 5: 112 peptides, 18 chains. Longest chain 13 peptides. Score 0.453 Taking the results from Round 2 Chains 17, Residues 96, Estimated correctness of the model 6.3 % 4 chains (21 residues) have been docked in sequence ------------------------------------------------------ 4637 reflections ( 99.83 % complete ) and 2968 restraints for refining 1387 atoms. 2531 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2811 (Rfree = 0.000) for 1387 atoms. Found 11 (12 requested) and removed 16 (6 requested) atoms. Cycle 37: After refmac, R = 0.2714 (Rfree = 0.000) for 1381 atoms. Found 6 (12 requested) and removed 6 (6 requested) atoms. Cycle 38: After refmac, R = 0.2725 (Rfree = 0.000) for 1379 atoms. Found 8 (12 requested) and removed 7 (6 requested) atoms. Cycle 39: After refmac, R = 0.2690 (Rfree = 0.000) for 1380 atoms. Found 8 (12 requested) and removed 6 (6 requested) atoms. Cycle 40: After refmac, R = 0.2602 (Rfree = 0.000) for 1379 atoms. Found 8 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.03 2.72 Search for helices and strands: 0 residues in 0 chains, 1427 seeds are put forward Round 1: 99 peptides, 16 chains. Longest chain 11 peptides. Score 0.426 Round 2: 113 peptides, 19 chains. Longest chain 11 peptides. Score 0.432 Round 3: 120 peptides, 17 chains. Longest chain 12 peptides. Score 0.526 Round 4: 116 peptides, 17 chains. Longest chain 23 peptides. Score 0.503 Round 5: 118 peptides, 18 chains. Longest chain 23 peptides. Score 0.489 Taking the results from Round 3 Chains 18, Residues 103, Estimated correctness of the model 19.5 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4637 reflections ( 99.83 % complete ) and 2953 restraints for refining 1387 atoms. 2520 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2769 (Rfree = 0.000) for 1387 atoms. Found 12 (12 requested) and removed 7 (6 requested) atoms. Cycle 42: After refmac, R = 0.2679 (Rfree = 0.000) for 1389 atoms. Found 12 (12 requested) and removed 6 (6 requested) atoms. Cycle 43: After refmac, R = 0.2624 (Rfree = 0.000) for 1393 atoms. Found 8 (12 requested) and removed 6 (6 requested) atoms. Cycle 44: After refmac, R = 0.2605 (Rfree = 0.000) for 1392 atoms. Found 11 (12 requested) and removed 6 (6 requested) atoms. Cycle 45: After refmac, R = 0.2550 (Rfree = 0.000) for 1396 atoms. Found 8 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.05 2.74 Search for helices and strands: 0 residues in 0 chains, 1457 seeds are put forward Round 1: 95 peptides, 17 chains. Longest chain 10 peptides. Score 0.370 Round 2: 106 peptides, 15 chains. Longest chain 18 peptides. Score 0.496 Round 3: 113 peptides, 17 chains. Longest chain 18 peptides. Score 0.485 Round 4: 102 peptides, 15 chains. Longest chain 14 peptides. Score 0.472 Round 5: 108 peptides, 16 chains. Longest chain 12 peptides. Score 0.482 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 15, Residues 91, Estimated correctness of the model 9.9 % 2 chains (23 residues) have been docked in sequence Sequence coverage is 25 % Consider running further cycles of model building using 2ou6-3_warpNtrace.pdb as input Building loops using Loopy2018 15 chains (91 residues) following loop building 2 chains (23 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4637 reflections ( 99.83 % complete ) and 2793 restraints for refining 1387 atoms. 2356 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2778 (Rfree = 0.000) for 1387 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.2775 (Rfree = 0.000) for 1376 atoms. Found 0 (12 requested) and removed 5 (6 requested) atoms. Cycle 48: After refmac, R = 0.2727 (Rfree = 0.000) for 1371 atoms. Found 0 (12 requested) and removed 3 (6 requested) atoms. Cycle 49: After refmac, R = 0.2673 (Rfree = 0.000) for 1366 atoms. TimeTaking 30.42