Sun 23 Dec 22:22:56 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 2hdo-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2hdo-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2hdo-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hdo-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/2hdo-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hdo-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 22:23:05 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/2hdo-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hdo-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 138 and 0 Target number of residues in the AU: 138 Target solvent content: 0.6389 Checking the provided sequence file Detected sequence length: 209 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 209 Adjusted target solvent content: 0.45 Input MTZ file: 2hdo-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: 169 Cell parameters: 87.040 87.040 47.290 90.000 90.000 120.000 Input sequence file: 2hdo-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 1672 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: 29.474 3.400 Wilson plot Bfac: 71.16 2897 reflections ( 99.66 % complete ) and 0 restraints for refining 1861 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Starting model: R = 0.3255 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2645 (Rfree = 0.000) for 1861 atoms. Found 14 (14 requested) and removed 16 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.35 3.58 Search for helices and strands: 0 residues in 0 chains, 1902 seeds are put forward Round 1: 75 peptides, 16 chains. Longest chain 8 peptides. Score 0.267 Round 2: 109 peptides, 19 chains. Longest chain 11 peptides. Score 0.438 Round 3: 121 peptides, 20 chains. Longest chain 13 peptides. Score 0.492 Round 4: 125 peptides, 15 chains. Longest chain 16 peptides. Score 0.646 Round 5: 127 peptides, 17 chains. Longest chain 16 peptides. Score 0.609 Taking the results from Round 4 Chains 15, Residues 110, Estimated correctness of the model 43.0 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 2897 reflections ( 99.66 % complete ) and 3187 restraints for refining 1521 atoms. 2719 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2280 (Rfree = 0.000) for 1521 atoms. Found 8 (11 requested) and removed 10 (5 requested) atoms. Cycle 2: After refmac, R = 0.2208 (Rfree = 0.000) for 1500 atoms. Found 6 (11 requested) and removed 10 (5 requested) atoms. Cycle 3: After refmac, R = 0.2179 (Rfree = 0.000) for 1480 atoms. Found 10 (11 requested) and removed 7 (5 requested) atoms. Cycle 4: After refmac, R = 0.1813 (Rfree = 0.000) for 1468 atoms. Found 5 (11 requested) and removed 7 (5 requested) atoms. Cycle 5: After refmac, R = 0.1726 (Rfree = 0.000) for 1459 atoms. Found 6 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.34 3.57 Search for helices and strands: 0 residues in 0 chains, 1537 seeds are put forward Round 1: 104 peptides, 18 chains. Longest chain 15 peptides. Score 0.432 Round 2: 122 peptides, 17 chains. Longest chain 15 peptides. Score 0.580 Round 3: 128 peptides, 17 chains. Longest chain 16 peptides. Score 0.615 Round 4: 123 peptides, 15 chains. Longest chain 16 peptides. Score 0.636 Round 5: 125 peptides, 15 chains. Longest chain 20 peptides. Score 0.646 Taking the results from Round 5 Chains 16, Residues 110, Estimated correctness of the model 43.0 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 2897 reflections ( 99.66 % complete ) and 3204 restraints for refining 1487 atoms. 2712 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2196 (Rfree = 0.000) for 1487 atoms. Found 7 (11 requested) and removed 15 (5 requested) atoms. Cycle 7: After refmac, R = 0.2011 (Rfree = 0.000) for 1472 atoms. Found 3 (11 requested) and removed 8 (5 requested) atoms. Cycle 8: After refmac, R = 0.1843 (Rfree = 0.000) for 1463 atoms. Found 1 (11 requested) and removed 5 (5 requested) atoms. Cycle 9: After refmac, R = 0.1876 (Rfree = 0.000) for 1457 atoms. Found 1 (11 requested) and removed 9 (5 requested) atoms. Cycle 10: After refmac, R = 0.1755 (Rfree = 0.000) for 1446 atoms. Found 1 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.33 3.56 Search for helices and strands: 0 residues in 0 chains, 1524 seeds are put forward Round 1: 112 peptides, 18 chains. Longest chain 16 peptides. Score 0.489 Round 2: 126 peptides, 17 chains. Longest chain 17 peptides. Score 0.603 Round 3: 134 peptides, 16 chains. Longest chain 19 peptides. Score 0.669 Round 4: 139 peptides, 13 chains. Longest chain 24 peptides. Score 0.751 Round 5: 146 peptides, 15 chains. Longest chain 28 peptides. Score 0.741 Taking the results from Round 4 Chains 16, Residues 126, Estimated correctness of the model 70.0 % 2 chains (29 residues) have been docked in sequence Building loops using Loopy2018 16 chains (126 residues) following loop building 2 chains (29 residues) in sequence following loop building ------------------------------------------------------ 2897 reflections ( 99.66 % complete ) and 3015 restraints for refining 1521 atoms. 2406 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2317 (Rfree = 0.000) for 1521 atoms. Found 11 (11 requested) and removed 14 (5 requested) atoms. Cycle 12: After refmac, R = 0.2073 (Rfree = 0.000) for 1512 atoms. Found 6 (11 requested) and removed 9 (5 requested) atoms. Cycle 13: After refmac, R = 0.2008 (Rfree = 0.000) for 1505 atoms. Found 3 (11 requested) and removed 9 (5 requested) atoms. Cycle 14: After refmac, R = 0.1860 (Rfree = 0.000) for 1495 atoms. Found 5 (10 requested) and removed 6 (5 requested) atoms. Failed to save intermediate PDB Cycle 15: After refmac, R = 0.1843 (Rfree = 0.000) for 1491 atoms. Found 4 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.34 3.57 Search for helices and strands: 0 residues in 0 chains, 1551 seeds are put forward Round 1: 138 peptides, 24 chains. Longest chain 19 peptides. Score 0.492 Round 2: 137 peptides, 17 chains. Longest chain 25 peptides. Score 0.661 Round 3: 137 peptides, 19 chains. Longest chain 16 peptides. Score 0.615 Round 4: 140 peptides, 17 chains. Longest chain 25 peptides. Score 0.676 Round 5: 142 peptides, 16 chains. Longest chain 17 peptides. Score 0.706 Taking the results from Round 5 Chains 16, Residues 126, Estimated correctness of the model 59.4 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 2897 reflections ( 99.66 % complete ) and 3190 restraints for refining 1520 atoms. 2671 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1946 (Rfree = 0.000) for 1520 atoms. Found 3 (10 requested) and removed 8 (5 requested) atoms. Cycle 17: After refmac, R = 0.1820 (Rfree = 0.000) for 1509 atoms. Found 5 (10 requested) and removed 7 (5 requested) atoms. Cycle 18: After refmac, R = 0.1647 (Rfree = 0.000) for 1505 atoms. Found 2 (9 requested) and removed 8 (5 requested) atoms. Cycle 19: After refmac, R = 0.1564 (Rfree = 0.000) for 1498 atoms. Found 4 (9 requested) and removed 6 (5 requested) atoms. Cycle 20: After refmac, R = 0.1541 (Rfree = 0.000) for 1495 atoms. Found 2 (9 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.33 3.56 Search for helices and strands: 0 residues in 0 chains, 1547 seeds are put forward Round 1: 99 peptides, 19 chains. Longest chain 12 peptides. Score 0.362 Round 2: 119 peptides, 18 chains. Longest chain 15 peptides. Score 0.535 Round 3: 114 peptides, 17 chains. Longest chain 14 peptides. Score 0.531 Round 4: 112 peptides, 17 chains. Longest chain 13 peptides. Score 0.518 Round 5: 122 peptides, 17 chains. Longest chain 14 peptides. Score 0.580 Taking the results from Round 5 Chains 17, Residues 105, Estimated correctness of the model 22.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2897 reflections ( 99.66 % complete ) and 3463 restraints for refining 1521 atoms. 3060 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1757 (Rfree = 0.000) for 1521 atoms. Found 7 (9 requested) and removed 5 (5 requested) atoms. Cycle 22: After refmac, R = 0.1603 (Rfree = 0.000) for 1519 atoms. Found 3 (9 requested) and removed 5 (5 requested) atoms. Cycle 23: After refmac, R = 0.1556 (Rfree = 0.000) for 1517 atoms. Found 2 (9 requested) and removed 6 (5 requested) atoms. Cycle 24: After refmac, R = 0.1532 (Rfree = 0.000) for 1512 atoms. Found 0 (9 requested) and removed 5 (5 requested) atoms. Cycle 25: After refmac, R = 0.1542 (Rfree = 0.000) for 1507 atoms. Found 0 (9 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.26 3.49 Search for helices and strands: 0 residues in 0 chains, 1581 seeds are put forward Round 1: 94 peptides, 18 chains. Longest chain 13 peptides. Score 0.356 Round 2: 117 peptides, 18 chains. Longest chain 14 peptides. Score 0.522 Round 3: 115 peptides, 17 chains. Longest chain 14 peptides. Score 0.537 Round 4: 123 peptides, 19 chains. Longest chain 12 peptides. Score 0.533 Round 5: 132 peptides, 22 chains. Longest chain 13 peptides. Score 0.508 Taking the results from Round 3 Chains 17, Residues 98, Estimated correctness of the model 6.8 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 2897 reflections ( 99.66 % complete ) and 3294 restraints for refining 1521 atoms. 2857 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1833 (Rfree = 0.000) for 1521 atoms. Found 7 (9 requested) and removed 7 (5 requested) atoms. Cycle 27: After refmac, R = 0.1686 (Rfree = 0.000) for 1519 atoms. Found 5 (9 requested) and removed 5 (5 requested) atoms. Cycle 28: After refmac, R = 0.1627 (Rfree = 0.000) for 1516 atoms. Found 1 (9 requested) and removed 6 (5 requested) atoms. Cycle 29: After refmac, R = 0.1620 (Rfree = 0.000) for 1511 atoms. Found 2 (9 requested) and removed 5 (5 requested) atoms. Cycle 30: After refmac, R = 0.1588 (Rfree = 0.000) for 1508 atoms. Found 2 (9 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.27 3.50 Search for helices and strands: 0 residues in 0 chains, 1568 seeds are put forward Round 1: 100 peptides, 17 chains. Longest chain 13 peptides. Score 0.434 Round 2: 110 peptides, 16 chains. Longest chain 14 peptides. Score 0.533 Round 3: 111 peptides, 16 chains. Longest chain 15 peptides. Score 0.540 Round 4: 103 peptides, 17 chains. Longest chain 13 peptides. Score 0.456 Round 5: 117 peptides, 17 chains. Longest chain 14 peptides. Score 0.550 Taking the results from Round 5 Chains 19, Residues 100, Estimated correctness of the model 11.5 % 2 chains (21 residues) have been docked in sequence ------------------------------------------------------ 2897 reflections ( 99.66 % complete ) and 3121 restraints for refining 1521 atoms. 2653 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1855 (Rfree = 0.000) for 1521 atoms. Found 6 (9 requested) and removed 7 (5 requested) atoms. Cycle 32: After refmac, R = 0.1838 (Rfree = 0.000) for 1512 atoms. Found 3 (9 requested) and removed 8 (5 requested) atoms. Cycle 33: After refmac, R = 0.1549 (Rfree = 0.000) for 1502 atoms. Found 2 (9 requested) and removed 6 (5 requested) atoms. Cycle 34: After refmac, R = 0.1517 (Rfree = 0.000) for 1497 atoms. Found 1 (9 requested) and removed 5 (5 requested) atoms. Cycle 35: After refmac, R = 0.1502 (Rfree = 0.000) for 1491 atoms. Found 3 (9 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.26 3.49 Search for helices and strands: 0 residues in 0 chains, 1537 seeds are put forward Round 1: 89 peptides, 16 chains. Longest chain 13 peptides. Score 0.383 Round 2: 106 peptides, 18 chains. Longest chain 11 peptides. Score 0.447 Round 3: 99 peptides, 14 chains. Longest chain 14 peptides. Score 0.519 Round 4: 100 peptides, 14 chains. Longest chain 13 peptides. Score 0.526 Round 5: 93 peptides, 13 chains. Longest chain 13 peptides. Score 0.509 Taking the results from Round 4 Chains 14, Residues 86, Estimated correctness of the model 2.7 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 2897 reflections ( 99.66 % complete ) and 3319 restraints for refining 1520 atoms. 2955 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1698 (Rfree = 0.000) for 1520 atoms. Found 5 (9 requested) and removed 7 (5 requested) atoms. Cycle 37: After refmac, R = 0.1569 (Rfree = 0.000) for 1516 atoms. Found 1 (9 requested) and removed 5 (5 requested) atoms. Cycle 38: After refmac, R = 0.1521 (Rfree = 0.000) for 1510 atoms. Found 2 (9 requested) and removed 5 (5 requested) atoms. Cycle 39: After refmac, R = 0.1478 (Rfree = 0.000) for 1507 atoms. Found 1 (9 requested) and removed 5 (5 requested) atoms. Cycle 40: After refmac, R = 0.1465 (Rfree = 0.000) for 1502 atoms. Found 2 (9 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.33 3.56 Search for helices and strands: 0 residues in 0 chains, 1549 seeds are put forward Round 1: 79 peptides, 16 chains. Longest chain 11 peptides. Score 0.302 Round 2: 89 peptides, 13 chains. Longest chain 13 peptides. Score 0.481 Round 3: 91 peptides, 15 chains. Longest chain 13 peptides. Score 0.431 Round 4: 86 peptides, 14 chains. Longest chain 11 peptides. Score 0.427 Round 5: 82 peptides, 14 chains. Longest chain 12 peptides. Score 0.396 Taking the results from Round 2 Chains 13, Residues 76, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 2897 reflections ( 99.66 % complete ) and 3461 restraints for refining 1521 atoms. 3156 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1594 (Rfree = 0.000) for 1521 atoms. Found 4 (9 requested) and removed 5 (5 requested) atoms. Cycle 42: After refmac, R = 0.1549 (Rfree = 0.000) for 1519 atoms. Found 3 (9 requested) and removed 5 (5 requested) atoms. Cycle 43: After refmac, R = 0.2394 (Rfree = 0.000) for 1515 atoms. Found 9 (9 requested) and removed 6 (5 requested) atoms. Cycle 44: After refmac, R = 0.1539 (Rfree = 0.000) for 1516 atoms. Found 2 (9 requested) and removed 6 (5 requested) atoms. Cycle 45: After refmac, R = 0.1747 (Rfree = 0.000) for 1512 atoms. Found 9 (9 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.30 3.53 Search for helices and strands: 0 residues in 0 chains, 1568 seeds are put forward Round 1: 78 peptides, 15 chains. Longest chain 9 peptides. Score 0.329 Round 2: 85 peptides, 15 chains. Longest chain 10 peptides. Score 0.385 Round 3: 85 peptides, 15 chains. Longest chain 11 peptides. Score 0.385 Round 4: 87 peptides, 15 chains. Longest chain 9 peptides. Score 0.401 Round 5: 87 peptides, 14 chains. Longest chain 11 peptides. Score 0.434 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 14, Residues 73, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence Sequence coverage is 8 % Consider running further cycles of model building using 2hdo-3_warpNtrace.pdb as input Building loops using Loopy2018 14 chains (73 residues) following loop building 2 chains (6 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2897 reflections ( 99.66 % complete ) and 3447 restraints for refining 1521 atoms. 3158 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1664 (Rfree = 0.000) for 1521 atoms. Found 0 (9 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.1528 (Rfree = 0.000) for 1513 atoms. Found 0 (9 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.1497 (Rfree = 0.000) for 1504 atoms. Found 0 (9 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.1302 (Rfree = 0.000) for 1497 atoms. TimeTaking 30.38