null Mon 24 Dec 07:36:55 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2ouw-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2ouw-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2ouw-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ouw-3.4-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2ouw-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ouw-3.4-parrot-noncs ############### 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 ============================================================ Mon 24 Dec 07:37:00 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/noncs/ArpWArp/wArpResults/WorkingDir/2ouw-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ouw-3.4-parrot-noncs/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 161 and 0 Target number of residues in the AU: 161 Target solvent content: 0.6455 Checking the provided sequence file Detected sequence length: 138 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 276 Adjusted target solvent content: 0.39 Input MTZ file: 2ouw-3.4-parrot-noncs.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: 182 Cell parameters: 62.683 62.683 216.710 90.000 90.000 120.000 Input sequence file: 2ouw-3.4-parrot-noncs.fasta_lf Building free atoms model in initial map for 2208 target number of atoms Had to go as low as 0.70 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: 108.355 3.400 Wilson plot Bfac: 74.07 3938 reflections ( 99.82 % complete ) and 0 restraints for refining 2456 atoms. Observations/parameters ratio is 0.40 ------------------------------------------------------ Starting model: R = 0.3541 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3194 (Rfree = 0.000) for 2456 atoms. Found 18 (18 requested) and removed 16 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.38 3.92 Search for helices and strands: 0 residues in 0 chains, 2510 seeds are put forward NCS extension: 0 residues added, 2510 seeds are put forward Round 1: 104 peptides, 22 chains. Longest chain 8 peptides. Score 0.285 Round 2: 114 peptides, 20 chains. Longest chain 8 peptides. Score 0.409 Round 3: 144 peptides, 20 chains. Longest chain 17 peptides. Score 0.579 Round 4: 146 peptides, 24 chains. Longest chain 12 peptides. Score 0.498 Round 5: 149 peptides, 19 chains. Longest chain 20 peptides. Score 0.624 Taking the results from Round 5 Chains 20, Residues 130, Estimated correctness of the model 36.3 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 3938 reflections ( 99.82 % complete ) and 4347 restraints for refining 2001 atoms. 3791 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3382 (Rfree = 0.000) for 2001 atoms. Found 12 (15 requested) and removed 45 (7 requested) atoms. Cycle 2: After refmac, R = 0.3519 (Rfree = 0.000) for 1925 atoms. Found 14 (14 requested) and removed 37 (7 requested) atoms. Cycle 3: After refmac, R = 0.3520 (Rfree = 0.000) for 1875 atoms. Found 14 (14 requested) and removed 30 (7 requested) atoms. Cycle 4: After refmac, R = 0.3604 (Rfree = 0.000) for 1845 atoms. Found 14 (14 requested) and removed 25 (7 requested) atoms. Cycle 5: After refmac, R = 0.3638 (Rfree = 0.000) for 1827 atoms. Found 13 (13 requested) and removed 29 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.20 3.71 Search for helices and strands: 0 residues in 0 chains, 1883 seeds are put forward NCS extension: 17 residues added (3 deleted due to clashes), 1900 seeds are put forward Round 1: 55 peptides, 13 chains. Longest chain 7 peptides. Score 0.193 Round 2: 83 peptides, 17 chains. Longest chain 8 peptides. Score 0.284 Round 3: 76 peptides, 15 chains. Longest chain 10 peptides. Score 0.294 Round 4: 74 peptides, 14 chains. Longest chain 9 peptides. Score 0.311 Round 5: 84 peptides, 15 chains. Longest chain 11 peptides. Score 0.352 Taking the results from Round 5 Chains 15, Residues 69, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3938 reflections ( 99.82 % complete ) and 4043 restraints for refining 1715 atoms. 3782 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3522 (Rfree = 0.000) for 1715 atoms. Found 12 (12 requested) and removed 28 (6 requested) atoms. Cycle 7: After refmac, R = 0.3524 (Rfree = 0.000) for 1691 atoms. Found 12 (12 requested) and removed 17 (6 requested) atoms. Cycle 8: After refmac, R = 0.3411 (Rfree = 0.000) for 1676 atoms. Found 12 (12 requested) and removed 22 (6 requested) atoms. Cycle 9: After refmac, R = 0.3417 (Rfree = 0.000) for 1659 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. Cycle 10: After refmac, R = 0.3326 (Rfree = 0.000) for 1657 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.12 3.62 Search for helices and strands: 0 residues in 0 chains, 1726 seeds are put forward NCS extension: 0 residues added, 1726 seeds are put forward Round 1: 66 peptides, 16 chains. Longest chain 5 peptides. Score 0.183 Round 2: 85 peptides, 17 chains. Longest chain 7 peptides. Score 0.298 Round 3: 79 peptides, 15 chains. Longest chain 8 peptides. Score 0.316 Round 4: 93 peptides, 20 chains. Longest chain 8 peptides. Score 0.265 Round 5: 97 peptides, 17 chains. Longest chain 11 peptides. Score 0.382 Taking the results from Round 5 Chains 17, Residues 80, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3938 reflections ( 99.82 % complete ) and 3172 restraints for refining 1550 atoms. 2869 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3295 (Rfree = 0.000) for 1550 atoms. Found 11 (11 requested) and removed 15 (5 requested) atoms. Cycle 12: After refmac, R = 0.3129 (Rfree = 0.000) for 1538 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 13: After refmac, R = 0.3205 (Rfree = 0.000) for 1534 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 14: After refmac, R = 0.3172 (Rfree = 0.000) for 1535 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 15: After refmac, R = 0.3173 (Rfree = 0.000) for 1529 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.19 3.70 Search for helices and strands: 0 residues in 0 chains, 1604 seeds are put forward NCS extension: 0 residues added, 1604 seeds are put forward Round 1: 101 peptides, 22 chains. Longest chain 9 peptides. Score 0.264 Round 2: 112 peptides, 20 chains. Longest chain 11 peptides. Score 0.396 Round 3: 107 peptides, 18 chains. Longest chain 11 peptides. Score 0.419 Round 4: 101 peptides, 20 chains. Longest chain 9 peptides. Score 0.322 Round 5: 110 peptides, 20 chains. Longest chain 10 peptides. Score 0.383 Taking the results from Round 3 Chains 18, Residues 89, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3938 reflections ( 99.82 % complete ) and 3306 restraints for refining 1584 atoms. 2968 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3056 (Rfree = 0.000) for 1584 atoms. Found 11 (11 requested) and removed 20 (5 requested) atoms. Cycle 17: After refmac, R = 0.2964 (Rfree = 0.000) for 1572 atoms. Found 10 (11 requested) and removed 8 (5 requested) atoms. Cycle 18: After refmac, R = 0.3038 (Rfree = 0.000) for 1570 atoms. Found 11 (11 requested) and removed 17 (5 requested) atoms. Cycle 19: After refmac, R = 0.3052 (Rfree = 0.000) for 1563 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 20: After refmac, R = 0.2757 (Rfree = 0.000) for 1563 atoms. Found 6 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.21 3.73 Search for helices and strands: 0 residues in 0 chains, 1634 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 1645 seeds are put forward Round 1: 93 peptides, 21 chains. Longest chain 6 peptides. Score 0.235 Round 2: 98 peptides, 18 chains. Longest chain 11 peptides. Score 0.360 Round 3: 99 peptides, 20 chains. Longest chain 9 peptides. Score 0.308 Round 4: 108 peptides, 21 chains. Longest chain 7 peptides. Score 0.341 Round 5: 101 peptides, 20 chains. Longest chain 7 peptides. Score 0.322 Taking the results from Round 2 Chains 18, Residues 80, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 3938 reflections ( 99.82 % complete ) and 3390 restraints for refining 1629 atoms. 3048 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3065 (Rfree = 0.000) for 1629 atoms. Found 10 (12 requested) and removed 15 (6 requested) atoms. Cycle 22: After refmac, R = 0.3204 (Rfree = 0.000) for 1621 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 23: After refmac, R = 0.3170 (Rfree = 0.000) for 1622 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 24: After refmac, R = 0.3199 (Rfree = 0.000) for 1623 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 25: After refmac, R = 0.3307 (Rfree = 0.000) for 1618 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.20 3.71 Search for helices and strands: 0 residues in 0 chains, 1676 seeds are put forward NCS extension: 0 residues added, 1676 seeds are put forward Round 1: 69 peptides, 14 chains. Longest chain 8 peptides. Score 0.273 Round 2: 80 peptides, 15 chains. Longest chain 9 peptides. Score 0.324 Round 3: 82 peptides, 14 chains. Longest chain 9 peptides. Score 0.368 Round 4: 80 peptides, 14 chains. Longest chain 10 peptides. Score 0.354 Round 5: 87 peptides, 16 chains. Longest chain 9 peptides. Score 0.343 Taking the results from Round 3 Chains 14, Residues 68, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3938 reflections ( 99.82 % complete ) and 3623 restraints for refining 1658 atoms. 3365 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3326 (Rfree = 0.000) for 1658 atoms. Found 12 (12 requested) and removed 17 (6 requested) atoms. Cycle 27: After refmac, R = 0.3338 (Rfree = 0.000) for 1645 atoms. Found 12 (12 requested) and removed 16 (6 requested) atoms. Cycle 28: After refmac, R = 0.3332 (Rfree = 0.000) for 1641 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 29: After refmac, R = 0.3329 (Rfree = 0.000) for 1643 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 30: After refmac, R = 0.3300 (Rfree = 0.000) for 1644 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.22 3.74 Search for helices and strands: 0 residues in 0 chains, 1726 seeds are put forward NCS extension: 0 residues added, 1726 seeds are put forward Round 1: 64 peptides, 14 chains. Longest chain 6 peptides. Score 0.234 Round 2: 75 peptides, 15 chains. Longest chain 10 peptides. Score 0.287 Round 3: 88 peptides, 17 chains. Longest chain 11 peptides. Score 0.320 Round 4: 97 peptides, 19 chains. Longest chain 9 peptides. Score 0.324 Round 5: 81 peptides, 15 chains. Longest chain 11 peptides. Score 0.331 Taking the results from Round 5 Chains 15, Residues 66, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3938 reflections ( 99.82 % complete ) and 3585 restraints for refining 1683 atoms. 3336 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3214 (Rfree = 0.000) for 1683 atoms. Found 12 (12 requested) and removed 18 (6 requested) atoms. Cycle 32: After refmac, R = 0.3314 (Rfree = 0.000) for 1671 atoms. Found 12 (12 requested) and removed 16 (6 requested) atoms. Cycle 33: After refmac, R = 0.3321 (Rfree = 0.000) for 1660 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 34: After refmac, R = 0.3323 (Rfree = 0.000) for 1658 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 35: After refmac, R = 0.3404 (Rfree = 0.000) for 1655 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.21 3.73 Search for helices and strands: 0 residues in 0 chains, 1729 seeds are put forward NCS extension: 0 residues added, 1729 seeds are put forward Round 1: 52 peptides, 12 chains. Longest chain 7 peptides. Score 0.203 Round 2: 79 peptides, 18 chains. Longest chain 8 peptides. Score 0.222 Round 3: 67 peptides, 15 chains. Longest chain 7 peptides. Score 0.225 Round 4: 72 peptides, 14 chains. Longest chain 11 peptides. Score 0.296 Round 5: 79 peptides, 15 chains. Longest chain 11 peptides. Score 0.316 Taking the results from Round 5 Chains 15, Residues 64, Estimated correctness of the model 0.0 % 2 chains (16 residues) have been docked in sequence ------------------------------------------------------ 3938 reflections ( 99.82 % complete ) and 3386 restraints for refining 1658 atoms. 3096 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3714 (Rfree = 0.000) for 1658 atoms. Found 12 (12 requested) and removed 32 (6 requested) atoms. Cycle 37: After refmac, R = 0.3464 (Rfree = 0.000) for 1633 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 38: After refmac, R = 0.3393 (Rfree = 0.000) for 1628 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 39: After refmac, R = 0.3415 (Rfree = 0.000) for 1623 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. Cycle 40: After refmac, R = 0.3074 (Rfree = 0.000) for 1616 atoms. Found 3 (12 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.24 3.76 Search for helices and strands: 0 residues in 0 chains, 1638 seeds are put forward NCS extension: 0 residues added, 1638 seeds are put forward Round 1: 72 peptides, 16 chains. Longest chain 6 peptides. Score 0.232 Round 2: 79 peptides, 14 chains. Longest chain 8 peptides. Score 0.347 Round 3: 79 peptides, 15 chains. Longest chain 10 peptides. Score 0.316 Round 4: 83 peptides, 14 chains. Longest chain 10 peptides. Score 0.375 Round 5: 86 peptides, 14 chains. Longest chain 14 peptides. Score 0.396 Taking the results from Round 5 Chains 14, Residues 72, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3938 reflections ( 99.82 % complete ) and 3501 restraints for refining 1658 atoms. 3227 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3406 (Rfree = 0.000) for 1658 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. Cycle 42: After refmac, R = 0.3333 (Rfree = 0.000) for 1649 atoms. Found 12 (12 requested) and removed 16 (6 requested) atoms. Cycle 43: After refmac, R = 0.3382 (Rfree = 0.000) for 1642 atoms. Found 12 (12 requested) and removed 20 (6 requested) atoms. Cycle 44: After refmac, R = 0.3309 (Rfree = 0.000) for 1628 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. Cycle 45: After refmac, R = 0.3295 (Rfree = 0.000) for 1623 atoms. Found 12 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.22 3.74 Search for helices and strands: 0 residues in 0 chains, 1695 seeds are put forward NCS extension: 0 residues added, 1695 seeds are put forward Round 1: 58 peptides, 13 chains. Longest chain 7 peptides. Score 0.219 Round 2: 67 peptides, 14 chains. Longest chain 8 peptides. Score 0.258 Round 3: 67 peptides, 13 chains. Longest chain 10 peptides. Score 0.291 Round 4: 75 peptides, 14 chains. Longest chain 9 peptides. Score 0.319 Round 5: 77 peptides, 13 chains. Longest chain 10 peptides. Score 0.364 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 13, Residues 64, 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 2ouw-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3938 reflections ( 99.82 % complete ) and 3607 restraints for refining 1685 atoms. 3364 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3607 (Rfree = 0.000) for 1685 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.3529 (Rfree = 0.000) for 1670 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.3514 (Rfree = 0.000) for 1659 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.3277 (Rfree = 0.000) for 1652 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:08:00 GMT 2018 Job finished. TimeTaking 31.07 Used memory is bytes: -286472