Sun 23 Dec 22:22:40 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 2nyh-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2nyh-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2nyh-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2nyh-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/2nyh-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2nyh-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 22:22:48 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/2nyh-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2nyh-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 208 and 0 Target number of residues in the AU: 208 Target solvent content: 0.5948 Checking the provided sequence file Detected sequence length: 117 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 234 Adjusted target solvent content: 0.54 Input MTZ file: 2nyh-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: 20 Cell parameters: 70.985 88.344 88.592 90.000 90.000 90.000 Input sequence file: 2nyh-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 1872 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 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 55.335 3.200 Wilson plot Bfac: 50.29 4738 reflections ( 98.30 % complete ) and 0 restraints for refining 2093 atoms. Observations/parameters ratio is 0.57 ------------------------------------------------------ Starting model: R = 0.3622 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3573 (Rfree = 0.000) for 2093 atoms. Found 18 (18 requested) and removed 14 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.10 2.94 Search for helices and strands: 0 residues in 0 chains, 2112 seeds are put forward NCS extension: 0 residues added, 2112 seeds are put forward Round 1: 74 peptides, 16 chains. Longest chain 7 peptides. Score 0.241 Round 2: 115 peptides, 23 chains. Longest chain 8 peptides. Score 0.318 Round 3: 122 peptides, 21 chains. Longest chain 9 peptides. Score 0.409 Round 4: 118 peptides, 19 chains. Longest chain 13 peptides. Score 0.436 Round 5: 125 peptides, 22 chains. Longest chain 15 peptides. Score 0.402 Taking the results from Round 4 Chains 19, Residues 99, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4738 reflections ( 98.30 % complete ) and 3772 restraints for refining 1708 atoms. 3395 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3301 (Rfree = 0.000) for 1708 atoms. Found 15 (15 requested) and removed 8 (7 requested) atoms. Cycle 2: After refmac, R = 0.3258 (Rfree = 0.000) for 1696 atoms. Found 15 (15 requested) and removed 13 (7 requested) atoms. Cycle 3: After refmac, R = 0.3054 (Rfree = 0.000) for 1689 atoms. Found 15 (15 requested) and removed 9 (7 requested) atoms. Cycle 4: After refmac, R = 0.3005 (Rfree = 0.000) for 1690 atoms. Found 15 (15 requested) and removed 7 (7 requested) atoms. Cycle 5: After refmac, R = 0.2862 (Rfree = 0.000) for 1693 atoms. Found 15 (15 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.96 2.81 Search for helices and strands: 0 residues in 0 chains, 1740 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 1752 seeds are put forward Round 1: 114 peptides, 24 chains. Longest chain 7 peptides. Score 0.285 Round 2: 129 peptides, 21 chains. Longest chain 16 peptides. Score 0.448 Round 3: 131 peptides, 22 chains. Longest chain 12 peptides. Score 0.436 Round 4: 127 peptides, 23 chains. Longest chain 9 peptides. Score 0.389 Round 5: 119 peptides, 20 chains. Longest chain 10 peptides. Score 0.417 Taking the results from Round 2 Chains 21, Residues 108, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4738 reflections ( 98.30 % complete ) and 3785 restraints for refining 1709 atoms. 3374 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2987 (Rfree = 0.000) for 1709 atoms. Found 15 (15 requested) and removed 14 (7 requested) atoms. Cycle 7: After refmac, R = 0.2884 (Rfree = 0.000) for 1707 atoms. Found 15 (15 requested) and removed 10 (7 requested) atoms. Cycle 8: After refmac, R = 0.2711 (Rfree = 0.000) for 1709 atoms. Found 15 (15 requested) and removed 10 (7 requested) atoms. Cycle 9: After refmac, R = 0.2686 (Rfree = 0.000) for 1712 atoms. Found 15 (15 requested) and removed 14 (7 requested) atoms. Cycle 10: After refmac, R = 0.2546 (Rfree = 0.000) for 1710 atoms. Found 15 (15 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.94 2.79 Search for helices and strands: 0 residues in 0 chains, 1756 seeds are put forward NCS extension: 0 residues added, 1756 seeds are put forward Round 1: 115 peptides, 23 chains. Longest chain 8 peptides. Score 0.318 Round 2: 125 peptides, 22 chains. Longest chain 10 peptides. Score 0.402 Round 3: 115 peptides, 18 chains. Longest chain 15 peptides. Score 0.443 Round 4: 120 peptides, 22 chains. Longest chain 9 peptides. Score 0.373 Round 5: 121 peptides, 22 chains. Longest chain 11 peptides. Score 0.379 Taking the results from Round 3 Chains 18, Residues 97, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4738 reflections ( 98.30 % complete ) and 3906 restraints for refining 1709 atoms. 3536 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2789 (Rfree = 0.000) for 1709 atoms. Found 13 (15 requested) and removed 8 (7 requested) atoms. Cycle 12: After refmac, R = 0.2731 (Rfree = 0.000) for 1707 atoms. Found 15 (15 requested) and removed 9 (7 requested) atoms. Cycle 13: After refmac, R = 0.2533 (Rfree = 0.000) for 1706 atoms. Found 12 (15 requested) and removed 7 (7 requested) atoms. Cycle 14: After refmac, R = 0.2482 (Rfree = 0.000) for 1709 atoms. Found 15 (15 requested) and removed 10 (7 requested) atoms. Failed to save intermediate PDB Cycle 15: After refmac, R = 0.2436 (Rfree = 0.000) for 1713 atoms. Found 12 (15 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.96 2.81 Search for helices and strands: 0 residues in 0 chains, 1766 seeds are put forward NCS extension: 0 residues added, 1766 seeds are put forward Round 1: 101 peptides, 21 chains. Longest chain 10 peptides. Score 0.282 Round 2: 130 peptides, 20 chains. Longest chain 15 peptides. Score 0.477 Round 3: 123 peptides, 21 chains. Longest chain 10 peptides. Score 0.415 Round 4: 116 peptides, 22 chains. Longest chain 11 peptides. Score 0.349 Round 5: 123 peptides, 22 chains. Longest chain 14 peptides. Score 0.391 Taking the results from Round 2 Chains 20, Residues 110, Estimated correctness of the model 3.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4738 reflections ( 98.30 % complete ) and 3618 restraints for refining 1709 atoms. 3198 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2584 (Rfree = 0.000) for 1709 atoms. Found 15 (15 requested) and removed 16 (7 requested) atoms. Cycle 17: After refmac, R = 0.2538 (Rfree = 0.000) for 1706 atoms. Found 15 (15 requested) and removed 7 (7 requested) atoms. Cycle 18: After refmac, R = 0.2384 (Rfree = 0.000) for 1714 atoms. Found 13 (15 requested) and removed 7 (7 requested) atoms. Cycle 19: After refmac, R = 0.2380 (Rfree = 0.000) for 1719 atoms. Found 15 (15 requested) and removed 8 (7 requested) atoms. Cycle 20: After refmac, R = 0.2321 (Rfree = 0.000) for 1724 atoms. Found 15 (15 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.96 2.81 Search for helices and strands: 0 residues in 0 chains, 1762 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 1784 seeds are put forward Round 1: 103 peptides, 18 chains. Longest chain 11 peptides. Score 0.374 Round 2: 112 peptides, 17 chains. Longest chain 13 peptides. Score 0.451 Round 3: 111 peptides, 16 chains. Longest chain 15 peptides. Score 0.470 Round 4: 108 peptides, 19 chains. Longest chain 12 peptides. Score 0.378 Round 5: 119 peptides, 21 chains. Longest chain 10 peptides. Score 0.392 Taking the results from Round 3 Chains 16, Residues 95, Estimated correctness of the model 1.4 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 4738 reflections ( 98.30 % complete ) and 3755 restraints for refining 1708 atoms. 3363 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2537 (Rfree = 0.000) for 1708 atoms. Found 15 (15 requested) and removed 8 (7 requested) atoms. Cycle 22: After refmac, R = 0.2360 (Rfree = 0.000) for 1712 atoms. Found 13 (15 requested) and removed 11 (7 requested) atoms. Cycle 23: After refmac, R = 0.2353 (Rfree = 0.000) for 1712 atoms. Found 13 (15 requested) and removed 7 (7 requested) atoms. Cycle 24: After refmac, R = 0.2215 (Rfree = 0.000) for 1715 atoms. Found 12 (15 requested) and removed 9 (7 requested) atoms. Cycle 25: After refmac, R = 0.2227 (Rfree = 0.000) for 1717 atoms. Found 9 (15 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.90 2.75 Search for helices and strands: 0 residues in 0 chains, 1754 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 1772 seeds are put forward Round 1: 98 peptides, 20 chains. Longest chain 8 peptides. Score 0.290 Round 2: 104 peptides, 19 chains. Longest chain 10 peptides. Score 0.354 Round 3: 101 peptides, 17 chains. Longest chain 11 peptides. Score 0.388 Round 4: 102 peptides, 19 chains. Longest chain 10 peptides. Score 0.342 Round 5: 103 peptides, 19 chains. Longest chain 9 peptides. Score 0.348 Taking the results from Round 3 Chains 17, Residues 84, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4738 reflections ( 98.30 % complete ) and 3809 restraints for refining 1709 atoms. 3490 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2450 (Rfree = 0.000) for 1709 atoms. Found 15 (15 requested) and removed 11 (7 requested) atoms. Cycle 27: After refmac, R = 0.2536 (Rfree = 0.000) for 1710 atoms. Found 15 (15 requested) and removed 10 (7 requested) atoms. Cycle 28: After refmac, R = 0.2365 (Rfree = 0.000) for 1712 atoms. Found 15 (15 requested) and removed 8 (7 requested) atoms. Cycle 29: After refmac, R = 0.2468 (Rfree = 0.000) for 1716 atoms. Found 12 (15 requested) and removed 9 (7 requested) atoms. Cycle 30: After refmac, R = 0.2708 (Rfree = 0.000) for 1717 atoms. Found 15 (15 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.02 2.86 Search for helices and strands: 0 residues in 0 chains, 1742 seeds are put forward NCS extension: 0 residues added, 1742 seeds are put forward Round 1: 87 peptides, 16 chains. Longest chain 8 peptides. Score 0.328 Round 2: 100 peptides, 17 chains. Longest chain 10 peptides. Score 0.382 Round 3: 101 peptides, 18 chains. Longest chain 11 peptides. Score 0.362 Round 4: 102 peptides, 17 chains. Longest chain 13 peptides. Score 0.394 Round 5: 93 peptides, 16 chains. Longest chain 13 peptides. Score 0.366 Taking the results from Round 4 Chains 17, Residues 85, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4738 reflections ( 98.30 % complete ) and 3917 restraints for refining 1709 atoms. 3594 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2790 (Rfree = 0.000) for 1709 atoms. Found 15 (15 requested) and removed 9 (7 requested) atoms. Cycle 32: After refmac, R = 0.2596 (Rfree = 0.000) for 1708 atoms. Found 15 (15 requested) and removed 7 (7 requested) atoms. Cycle 33: After refmac, R = 0.2411 (Rfree = 0.000) for 1705 atoms. Found 15 (15 requested) and removed 9 (7 requested) atoms. Cycle 34: After refmac, R = 0.2561 (Rfree = 0.000) for 1709 atoms. Found 15 (15 requested) and removed 7 (7 requested) atoms. Cycle 35: After refmac, R = 0.2479 (Rfree = 0.000) for 1716 atoms. Found 15 (15 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.99 2.83 Search for helices and strands: 0 residues in 0 chains, 1756 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 1774 seeds are put forward Round 1: 78 peptides, 16 chains. Longest chain 10 peptides. Score 0.269 Round 2: 85 peptides, 18 chains. Longest chain 7 peptides. Score 0.259 Round 3: 93 peptides, 15 chains. Longest chain 10 peptides. Score 0.393 Round 4: 87 peptides, 16 chains. Longest chain 9 peptides. Score 0.328 Round 5: 100 peptides, 16 chains. Longest chain 10 peptides. Score 0.408 Taking the results from Round 5 Chains 16, Residues 84, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4738 reflections ( 98.30 % complete ) and 3803 restraints for refining 1709 atoms. 3483 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2653 (Rfree = 0.000) for 1709 atoms. Found 15 (15 requested) and removed 7 (7 requested) atoms. Cycle 37: After refmac, R = 0.2512 (Rfree = 0.000) for 1712 atoms. Found 15 (15 requested) and removed 7 (7 requested) atoms. Cycle 38: After refmac, R = 0.2660 (Rfree = 0.000) for 1714 atoms. Found 15 (15 requested) and removed 7 (7 requested) atoms. Cycle 39: After refmac, R = 0.2352 (Rfree = 0.000) for 1714 atoms. Found 15 (15 requested) and removed 7 (7 requested) atoms. Cycle 40: After refmac, R = 0.2452 (Rfree = 0.000) for 1718 atoms. Found 15 (15 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.95 2.80 Search for helices and strands: 0 residues in 0 chains, 1759 seeds are put forward NCS extension: 0 residues added, 1759 seeds are put forward Round 1: 87 peptides, 17 chains. Longest chain 12 peptides. Score 0.301 Round 2: 110 peptides, 20 chains. Longest chain 19 peptides. Score 0.364 Round 3: 94 peptides, 13 chains. Longest chain 19 peptides. Score 0.451 Round 4: 105 peptides, 15 chains. Longest chain 19 peptides. Score 0.462 Round 5: 105 peptides, 15 chains. Longest chain 19 peptides. Score 0.462 Taking the results from Round 5 Chains 15, Residues 90, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4738 reflections ( 98.30 % complete ) and 3956 restraints for refining 1709 atoms. 3611 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2578 (Rfree = 0.000) for 1709 atoms. Found 15 (15 requested) and removed 7 (7 requested) atoms. Cycle 42: After refmac, R = 0.2392 (Rfree = 0.000) for 1710 atoms. Found 15 (15 requested) and removed 7 (7 requested) atoms. Cycle 43: After refmac, R = 0.2337 (Rfree = 0.000) for 1717 atoms. Found 15 (15 requested) and removed 7 (7 requested) atoms. Cycle 44: After refmac, R = 0.2231 (Rfree = 0.000) for 1725 atoms. Found 15 (15 requested) and removed 7 (7 requested) atoms. Cycle 45: After refmac, R = 0.2345 (Rfree = 0.000) for 1727 atoms. Found 15 (15 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.95 2.80 Search for helices and strands: 0 residues in 0 chains, 1762 seeds are put forward NCS extension: 0 residues added, 1762 seeds are put forward Round 1: 91 peptides, 18 chains. Longest chain 12 peptides. Score 0.299 Round 2: 103 peptides, 16 chains. Longest chain 14 peptides. Score 0.425 Round 3: 106 peptides, 19 chains. Longest chain 10 peptides. Score 0.366 Round 4: 110 peptides, 19 chains. Longest chain 17 peptides. Score 0.390 Round 5: 98 peptides, 16 chains. Longest chain 17 peptides. Score 0.396 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 16, Residues 87, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2nyh-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4738 reflections ( 98.30 % complete ) and 3806 restraints for refining 1709 atoms. 3474 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2439 (Rfree = 0.000) for 1709 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.2510 (Rfree = 0.000) for 1695 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.2438 (Rfree = 0.000) for 1688 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.2468 (Rfree = 0.000) for 1679 atoms. TimeTaking 31.93