Sun 23 Dec 22:22:43 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 2nlv-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2nlv-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2nlv-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2nlv-3.8-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/2nlv-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2nlv-3.8-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 22:22:53 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/2nlv-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2nlv-3.8-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 145 and 0 Target number of residues in the AU: 145 Target solvent content: 0.6436 Checking the provided sequence file Detected sequence length: 112 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 224 Adjusted target solvent content: 0.45 Input MTZ file: 2nlv-3.8-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: 4 Cell parameters: 46.793 37.359 63.476 90.000 97.240 90.000 Input sequence file: 2nlv-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 1792 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 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: 29.104 3.800 Wilson plot Bfac: 73.11 2254 reflections ( 99.73 % complete ) and 0 restraints for refining 1990 atoms. Observations/parameters ratio is 0.28 ------------------------------------------------------ Starting model: R = 0.3629 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2589 (Rfree = 0.000) for 1990 atoms. Found 5 (10 requested) and removed 11 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.50 3.74 Search for helices and strands: 0 residues in 0 chains, 2019 seeds are put forward NCS extension: 0 residues added, 2019 seeds are put forward Round 1: 80 peptides, 17 chains. Longest chain 9 peptides. Score 0.269 Round 2: 93 peptides, 15 chains. Longest chain 21 peptides. Score 0.433 Round 3: 104 peptides, 18 chains. Longest chain 12 peptides. Score 0.420 Round 4: 106 peptides, 16 chains. Longest chain 12 peptides. Score 0.492 Round 5: 103 peptides, 13 chains. Longest chain 15 peptides. Score 0.556 Taking the results from Round 5 Chains 13, Residues 90, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2254 reflections ( 99.73 % complete ) and 3910 restraints for refining 1620 atoms. 3563 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2974 (Rfree = 0.000) for 1620 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 2: After refmac, R = 0.2828 (Rfree = 0.000) for 1622 atoms. Found 4 (8 requested) and removed 5 (4 requested) atoms. Cycle 3: After refmac, R = 0.2780 (Rfree = 0.000) for 1619 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 4: After refmac, R = 0.2710 (Rfree = 0.000) for 1615 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 5: After refmac, R = 0.2660 (Rfree = 0.000) for 1610 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.50 3.74 Search for helices and strands: 0 residues in 0 chains, 1647 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 1661 seeds are put forward Round 1: 77 peptides, 16 chains. Longest chain 8 peptides. Score 0.279 Round 2: 74 peptides, 13 chains. Longest chain 8 peptides. Score 0.357 Round 3: 87 peptides, 13 chains. Longest chain 10 peptides. Score 0.453 Round 4: 83 peptides, 14 chains. Longest chain 9 peptides. Score 0.393 Round 5: 94 peptides, 16 chains. Longest chain 13 peptides. Score 0.410 Taking the results from Round 3 Chains 13, Residues 74, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2254 reflections ( 99.73 % complete ) and 3934 restraints for refining 1591 atoms. 3651 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3011 (Rfree = 0.000) for 1591 atoms. Found 6 (8 requested) and removed 6 (4 requested) atoms. Cycle 7: After refmac, R = 0.2888 (Rfree = 0.000) for 1591 atoms. Found 1 (8 requested) and removed 4 (4 requested) atoms. Cycle 8: After refmac, R = 0.2795 (Rfree = 0.000) for 1585 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 9: After refmac, R = 0.2736 (Rfree = 0.000) for 1581 atoms. Found 1 (8 requested) and removed 4 (4 requested) atoms. Cycle 10: After refmac, R = 0.2668 (Rfree = 0.000) for 1577 atoms. Found 2 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.47 3.71 Search for helices and strands: 0 residues in 0 chains, 1607 seeds are put forward NCS extension: 0 residues added, 1607 seeds are put forward Round 1: 81 peptides, 16 chains. Longest chain 8 peptides. Score 0.311 Round 2: 103 peptides, 15 chains. Longest chain 17 peptides. Score 0.501 Round 3: 110 peptides, 18 chains. Longest chain 12 peptides. Score 0.461 Round 4: 104 peptides, 15 chains. Longest chain 15 peptides. Score 0.507 Round 5: 99 peptides, 18 chains. Longest chain 14 peptides. Score 0.384 Taking the results from Round 4 Chains 15, Residues 89, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2254 reflections ( 99.73 % complete ) and 3850 restraints for refining 1618 atoms. 3509 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3119 (Rfree = 0.000) for 1618 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 12: After refmac, R = 0.2939 (Rfree = 0.000) for 1616 atoms. Found 3 (8 requested) and removed 8 (4 requested) atoms. Cycle 13: After refmac, R = 0.2821 (Rfree = 0.000) for 1610 atoms. Found 1 (8 requested) and removed 5 (4 requested) atoms. Cycle 14: After refmac, R = 0.2815 (Rfree = 0.000) for 1606 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 15: After refmac, R = 0.2677 (Rfree = 0.000) for 1601 atoms. Found 1 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.53 3.77 Search for helices and strands: 0 residues in 0 chains, 1643 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 1669 seeds are put forward Round 1: 97 peptides, 21 chains. Longest chain 9 peptides. Score 0.273 Round 2: 99 peptides, 20 chains. Longest chain 9 peptides. Score 0.321 Round 3: 106 peptides, 19 chains. Longest chain 15 peptides. Score 0.404 Round 4: 107 peptides, 21 chains. Longest chain 9 peptides. Score 0.350 Round 5: 102 peptides, 18 chains. Longest chain 11 peptides. Score 0.405 Taking the results from Round 5 Chains 18, Residues 84, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2254 reflections ( 99.73 % complete ) and 3866 restraints for refining 1618 atoms. 3548 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2848 (Rfree = 0.000) for 1618 atoms. Found 4 (8 requested) and removed 6 (4 requested) atoms. Cycle 17: After refmac, R = 0.2757 (Rfree = 0.000) for 1615 atoms. Found 1 (8 requested) and removed 5 (4 requested) atoms. Cycle 18: After refmac, R = 0.2709 (Rfree = 0.000) for 1611 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 19: After refmac, R = 0.2702 (Rfree = 0.000) for 1607 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 20: After refmac, R = 0.2636 (Rfree = 0.000) for 1601 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.47 3.71 Search for helices and strands: 0 residues in 0 chains, 1636 seeds are put forward NCS extension: 5 residues added (2 deleted due to clashes), 1641 seeds are put forward Round 1: 91 peptides, 19 chains. Longest chain 8 peptides. Score 0.291 Round 2: 101 peptides, 19 chains. Longest chain 9 peptides. Score 0.367 Round 3: 92 peptides, 15 chains. Longest chain 11 peptides. Score 0.426 Round 4: 90 peptides, 13 chains. Longest chain 15 peptides. Score 0.473 Round 5: 105 peptides, 15 chains. Longest chain 22 peptides. Score 0.513 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 ------------------------------------------------------ 2254 reflections ( 99.73 % complete ) and 3854 restraints for refining 1620 atoms. 3509 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2795 (Rfree = 0.000) for 1620 atoms. Found 3 (8 requested) and removed 6 (4 requested) atoms. Cycle 22: After refmac, R = 0.2634 (Rfree = 0.000) for 1615 atoms. Found 1 (8 requested) and removed 4 (4 requested) atoms. Cycle 23: After refmac, R = 0.2595 (Rfree = 0.000) for 1611 atoms. Found 2 (8 requested) and removed 4 (4 requested) atoms. Cycle 24: After refmac, R = 0.2573 (Rfree = 0.000) for 1609 atoms. Found 1 (8 requested) and removed 4 (4 requested) atoms. Cycle 25: After refmac, R = 0.2515 (Rfree = 0.000) for 1605 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.48 3.72 Search for helices and strands: 0 residues in 0 chains, 1645 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 1666 seeds are put forward Round 1: 71 peptides, 16 chains. Longest chain 6 peptides. Score 0.229 Round 2: 85 peptides, 16 chains. Longest chain 8 peptides. Score 0.343 Round 3: 86 peptides, 14 chains. Longest chain 16 peptides. Score 0.415 Round 4: 95 peptides, 15 chains. Longest chain 17 peptides. Score 0.447 Round 5: 95 peptides, 14 chains. Longest chain 18 peptides. Score 0.477 Taking the results from Round 5 Chains 14, Residues 81, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2254 reflections ( 99.73 % complete ) and 3842 restraints for refining 1620 atoms. 3532 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2699 (Rfree = 0.000) for 1620 atoms. Found 3 (8 requested) and removed 4 (4 requested) atoms. Cycle 27: After refmac, R = 0.2637 (Rfree = 0.000) for 1619 atoms. Found 1 (8 requested) and removed 4 (4 requested) atoms. Cycle 28: After refmac, R = 0.2618 (Rfree = 0.000) for 1615 atoms. Found 3 (8 requested) and removed 4 (4 requested) atoms. Cycle 29: After refmac, R = 0.2594 (Rfree = 0.000) for 1614 atoms. Found 1 (8 requested) and removed 4 (4 requested) atoms. Cycle 30: After refmac, R = 0.2552 (Rfree = 0.000) for 1611 atoms. Found 1 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.50 3.74 Search for helices and strands: 0 residues in 0 chains, 1648 seeds are put forward NCS extension: 0 residues added, 1648 seeds are put forward Round 1: 75 peptides, 16 chains. Longest chain 6 peptides. Score 0.262 Round 2: 95 peptides, 19 chains. Longest chain 8 peptides. Score 0.322 Round 3: 90 peptides, 16 chains. Longest chain 14 peptides. Score 0.380 Round 4: 95 peptides, 16 chains. Longest chain 10 peptides. Score 0.417 Round 5: 95 peptides, 15 chains. Longest chain 17 peptides. Score 0.447 Taking the results from Round 5 Chains 15, Residues 80, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2254 reflections ( 99.73 % complete ) and 3925 restraints for refining 1620 atoms. 3620 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2697 (Rfree = 0.000) for 1620 atoms. Found 4 (8 requested) and removed 5 (4 requested) atoms. Cycle 32: After refmac, R = 0.2554 (Rfree = 0.000) for 1619 atoms. Found 3 (8 requested) and removed 4 (4 requested) atoms. Cycle 33: After refmac, R = 0.2478 (Rfree = 0.000) for 1616 atoms. Found 1 (8 requested) and removed 5 (4 requested) atoms. Cycle 34: After refmac, R = 0.2431 (Rfree = 0.000) for 1612 atoms. Found 1 (8 requested) and removed 4 (4 requested) atoms. Cycle 35: After refmac, R = 0.2419 (Rfree = 0.000) for 1609 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.47 3.71 Search for helices and strands: 0 residues in 0 chains, 1658 seeds are put forward NCS extension: 27 residues added (0 deleted due to clashes), 1685 seeds are put forward Round 1: 87 peptides, 16 chains. Longest chain 15 peptides. Score 0.358 Round 2: 80 peptides, 16 chains. Longest chain 7 peptides. Score 0.303 Round 3: 82 peptides, 17 chains. Longest chain 7 peptides. Score 0.286 Round 4: 75 peptides, 14 chains. Longest chain 9 peptides. Score 0.331 Round 5: 83 peptides, 16 chains. Longest chain 9 peptides. Score 0.327 Taking the results from Round 1 Chains 16, Residues 71, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2254 reflections ( 99.73 % complete ) and 3955 restraints for refining 1620 atoms. 3687 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2556 (Rfree = 0.000) for 1620 atoms. Found 5 (8 requested) and removed 4 (4 requested) atoms. Cycle 37: After refmac, R = 0.2439 (Rfree = 0.000) for 1621 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 38: After refmac, R = 0.2416 (Rfree = 0.000) for 1617 atoms. Found 1 (8 requested) and removed 4 (4 requested) atoms. Cycle 39: After refmac, R = 0.2375 (Rfree = 0.000) for 1614 atoms. Found 1 (8 requested) and removed 4 (4 requested) atoms. Cycle 40: After refmac, R = 0.2335 (Rfree = 0.000) for 1610 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.51 3.75 Search for helices and strands: 0 residues in 0 chains, 1644 seeds are put forward NCS extension: 0 residues added, 1644 seeds are put forward Round 1: 63 peptides, 13 chains. Longest chain 11 peptides. Score 0.267 Round 2: 74 peptides, 13 chains. Longest chain 16 peptides. Score 0.357 Round 3: 80 peptides, 14 chains. Longest chain 10 peptides. Score 0.370 Round 4: 75 peptides, 13 chains. Longest chain 12 peptides. Score 0.365 Round 5: 70 peptides, 12 chains. Longest chain 10 peptides. Score 0.360 Taking the results from Round 3 Chains 14, Residues 66, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 2254 reflections ( 99.73 % complete ) and 3994 restraints for refining 1611 atoms. 3744 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2539 (Rfree = 0.000) for 1611 atoms. Found 8 (8 requested) and removed 4 (4 requested) atoms. Cycle 42: After refmac, R = 0.2422 (Rfree = 0.000) for 1615 atoms. Found 2 (8 requested) and removed 4 (4 requested) atoms. Cycle 43: After refmac, R = 0.2539 (Rfree = 0.000) for 1612 atoms. Found 1 (8 requested) and removed 4 (4 requested) atoms. Cycle 44: After refmac, R = 0.2515 (Rfree = 0.000) for 1609 atoms. Found 2 (8 requested) and removed 4 (4 requested) atoms. Cycle 45: After refmac, R = 0.2532 (Rfree = 0.000) for 1607 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.50 3.74 Search for helices and strands: 0 residues in 0 chains, 1641 seeds are put forward NCS extension: 0 residues added, 1641 seeds are put forward Round 1: 62 peptides, 12 chains. Longest chain 9 peptides. Score 0.295 Round 2: 68 peptides, 12 chains. Longest chain 10 peptides. Score 0.344 Round 3: 59 peptides, 11 chains. Longest chain 10 peptides. Score 0.306 Round 4: 60 peptides, 9 chains. Longest chain 13 peptides. Score 0.387 Round 5: 59 peptides, 12 chains. Longest chain 8 peptides. Score 0.269 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 9, Residues 51, 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 2nlv-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2254 reflections ( 99.73 % complete ) and 4068 restraints for refining 1620 atoms. 3873 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2672 (Rfree = 0.000) for 1620 atoms. Found 0 (8 requested) and removed 1 (4 requested) atoms. Cycle 47: After refmac, R = 0.2396 (Rfree = 0.000) for 1618 atoms. Found 0 (8 requested) and removed 1 (4 requested) atoms. Cycle 48: After refmac, R = 0.2635 (Rfree = 0.000) for 1617 atoms. Found 0 (8 requested) and removed 1 (4 requested) atoms. Cycle 49: After refmac, R = 0.2653 (Rfree = 0.000) for 1616 atoms. TimeTaking 28.1