Sun 23 Dec 22:22:49 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-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2nyh-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2nyh-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2nyh-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/2nyh-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2nyh-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 22:22:58 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-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2nyh-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 185 and 0 Target number of residues in the AU: 185 Target solvent content: 0.6396 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-3.8-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: 20 Cell parameters: 70.985 88.344 88.592 90.000 90.000 90.000 Input sequence file: 2nyh-3.8-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 3.802 Wilson plot Bfac: 71.07 2851 reflections ( 97.87 % complete ) and 0 restraints for refining 2066 atoms. Observations/parameters ratio is 0.34 ------------------------------------------------------ Starting model: R = 0.3570 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3389 (Rfree = 0.000) for 2066 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.69 3.50 Search for helices and strands: 0 residues in 0 chains, 2086 seeds are put forward NCS extension: 0 residues added, 2086 seeds are put forward Round 1: 71 peptides, 15 chains. Longest chain 9 peptides. Score 0.249 Round 2: 94 peptides, 18 chains. Longest chain 9 peptides. Score 0.318 Round 3: 99 peptides, 20 chains. Longest chain 8 peptides. Score 0.296 Round 4: 113 peptides, 19 chains. Longest chain 11 peptides. Score 0.407 Round 5: 119 peptides, 21 chains. Longest chain 11 peptides. Score 0.392 Taking the results from Round 4 Chains 19, Residues 94, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2851 reflections ( 97.87 % complete ) and 3844 restraints for refining 1646 atoms. 3487 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3356 (Rfree = 0.000) for 1646 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. Cycle 2: After refmac, R = 0.3313 (Rfree = 0.000) for 1628 atoms. Found 8 (9 requested) and removed 5 (4 requested) atoms. Cycle 3: After refmac, R = 0.3254 (Rfree = 0.000) for 1603 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 4: After refmac, R = 0.3418 (Rfree = 0.000) for 1579 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 5: After refmac, R = 0.3300 (Rfree = 0.000) for 1560 atoms. Found 7 (8 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.55 3.37 Search for helices and strands: 0 residues in 0 chains, 1598 seeds are put forward NCS extension: 0 residues added, 1598 seeds are put forward Round 1: 92 peptides, 19 chains. Longest chain 7 peptides. Score 0.278 Round 2: 100 peptides, 16 chains. Longest chain 12 peptides. Score 0.408 Round 3: 110 peptides, 17 chains. Longest chain 12 peptides. Score 0.440 Round 4: 112 peptides, 17 chains. Longest chain 10 peptides. Score 0.451 Round 5: 116 peptides, 17 chains. Longest chain 14 peptides. Score 0.473 Taking the results from Round 5 Chains 17, Residues 99, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 2851 reflections ( 97.87 % complete ) and 3492 restraints for refining 1585 atoms. 3075 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3426 (Rfree = 0.000) for 1585 atoms. Found 8 (8 requested) and removed 15 (4 requested) atoms. Cycle 7: After refmac, R = 0.3228 (Rfree = 0.000) for 1555 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 8: After refmac, R = 0.2966 (Rfree = 0.000) for 1540 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 9: After refmac, R = 0.3261 (Rfree = 0.000) for 1528 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. Cycle 10: After refmac, R = 0.3122 (Rfree = 0.000) for 1515 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.54 3.36 Search for helices and strands: 0 residues in 0 chains, 1547 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 1568 seeds are put forward Round 1: 90 peptides, 20 chains. Longest chain 7 peptides. Score 0.237 Round 2: 95 peptides, 17 chains. Longest chain 10 peptides. Score 0.352 Round 3: 108 peptides, 18 chains. Longest chain 11 peptides. Score 0.404 Round 4: 112 peptides, 20 chains. Longest chain 10 peptides. Score 0.376 Round 5: 117 peptides, 18 chains. Longest chain 17 peptides. Score 0.454 Taking the results from Round 5 Chains 18, Residues 99, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2851 reflections ( 97.87 % complete ) and 3783 restraints for refining 1657 atoms. 3405 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3197 (Rfree = 0.000) for 1657 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 12: After refmac, R = 0.3096 (Rfree = 0.000) for 1633 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 13: After refmac, R = 0.2884 (Rfree = 0.000) for 1611 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. Cycle 14: After refmac, R = 0.3140 (Rfree = 0.000) for 1594 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Cycle 15: After refmac, R = 0.2964 (Rfree = 0.000) for 1580 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.49 3.31 Search for helices and strands: 0 residues in 0 chains, 1612 seeds are put forward NCS extension: 0 residues added, 1612 seeds are put forward Round 1: 91 peptides, 18 chains. Longest chain 9 peptides. Score 0.299 Round 2: 101 peptides, 16 chains. Longest chain 11 peptides. Score 0.414 Round 3: 103 peptides, 19 chains. Longest chain 10 peptides. Score 0.348 Round 4: 109 peptides, 19 chains. Longest chain 10 peptides. Score 0.384 Round 5: 115 peptides, 19 chains. Longest chain 16 peptides. Score 0.419 Taking the results from Round 5 Chains 19, Residues 96, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2851 reflections ( 97.87 % complete ) and 3833 restraints for refining 1662 atoms. 3468 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3056 (Rfree = 0.000) for 1662 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. Cycle 17: After refmac, R = 0.3100 (Rfree = 0.000) for 1644 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Cycle 18: After refmac, R = 0.3014 (Rfree = 0.000) for 1619 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 19: After refmac, R = 0.2863 (Rfree = 0.000) for 1601 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 20: After refmac, R = 0.2888 (Rfree = 0.000) for 1592 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.56 3.37 Search for helices and strands: 0 residues in 0 chains, 1613 seeds are put forward NCS extension: 0 residues added, 1613 seeds are put forward Round 1: 92 peptides, 19 chains. Longest chain 7 peptides. Score 0.278 Round 2: 111 peptides, 19 chains. Longest chain 12 peptides. Score 0.396 Round 3: 106 peptides, 17 chains. Longest chain 10 peptides. Score 0.417 Round 4: 114 peptides, 16 chains. Longest chain 13 peptides. Score 0.486 Round 5: 105 peptides, 16 chains. Longest chain 13 peptides. Score 0.437 Taking the results from Round 4 Chains 16, Residues 98, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2851 reflections ( 97.87 % complete ) and 3605 restraints for refining 1641 atoms. 3229 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3083 (Rfree = 0.000) for 1641 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 22: After refmac, R = 0.3078 (Rfree = 0.000) for 1605 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 23: After refmac, R = 0.2708 (Rfree = 0.000) for 1588 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. Cycle 24: After refmac, R = 0.2950 (Rfree = 0.000) for 1574 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 25: After refmac, R = 0.2922 (Rfree = 0.000) for 1570 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.54 3.36 Search for helices and strands: 0 residues in 0 chains, 1598 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 1611 seeds are put forward Round 1: 84 peptides, 16 chains. Longest chain 9 peptides. Score 0.309 Round 2: 87 peptides, 13 chains. Longest chain 14 peptides. Score 0.410 Round 3: 88 peptides, 13 chains. Longest chain 14 peptides. Score 0.416 Round 4: 95 peptides, 12 chains. Longest chain 15 peptides. Score 0.482 Round 5: 98 peptides, 16 chains. Longest chain 15 peptides. Score 0.396 Taking the results from Round 4 Chains 12, Residues 83, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2851 reflections ( 97.87 % complete ) and 3627 restraints for refining 1634 atoms. 3307 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3175 (Rfree = 0.000) for 1634 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Cycle 27: After refmac, R = 0.3110 (Rfree = 0.000) for 1615 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 28: After refmac, R = 0.3040 (Rfree = 0.000) for 1596 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.2605 (Rfree = 0.000) for 1585 atoms. Found 8 (8 requested) and removed 4 (4 requested) atoms. Cycle 30: After refmac, R = 0.2952 (Rfree = 0.000) for 1576 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.50 3.32 Search for helices and strands: 0 residues in 0 chains, 1602 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 1624 seeds are put forward Round 1: 69 peptides, 13 chains. Longest chain 15 peptides. Score 0.295 Round 2: 79 peptides, 14 chains. Longest chain 10 peptides. Score 0.333 Round 3: 87 peptides, 14 chains. Longest chain 11 peptides. Score 0.383 Round 4: 102 peptides, 17 chains. Longest chain 17 peptides. Score 0.394 Round 5: 98 peptides, 17 chains. Longest chain 9 peptides. Score 0.370 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 ------------------------------------------------------ 2851 reflections ( 97.87 % complete ) and 3485 restraints for refining 1603 atoms. 3162 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3111 (Rfree = 0.000) for 1603 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Cycle 32: After refmac, R = 0.2991 (Rfree = 0.000) for 1580 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Cycle 33: After refmac, R = 0.2885 (Rfree = 0.000) for 1551 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Cycle 34: After refmac, R = 0.2986 (Rfree = 0.000) for 1534 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. Cycle 35: After refmac, R = 0.2881 (Rfree = 0.000) for 1523 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.59 3.40 Search for helices and strands: 0 residues in 0 chains, 1539 seeds are put forward NCS extension: 0 residues added, 1539 seeds are put forward Round 1: 70 peptides, 14 chains. Longest chain 9 peptides. Score 0.272 Round 2: 87 peptides, 16 chains. Longest chain 11 peptides. Score 0.328 Round 3: 78 peptides, 13 chains. Longest chain 10 peptides. Score 0.355 Round 4: 90 peptides, 16 chains. Longest chain 9 peptides. Score 0.347 Round 5: 88 peptides, 17 chains. Longest chain 12 peptides. Score 0.307 Taking the results from Round 3 Chains 13, Residues 65, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2851 reflections ( 97.87 % complete ) and 3354 restraints for refining 1523 atoms. 3107 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3008 (Rfree = 0.000) for 1523 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. Cycle 37: After refmac, R = 0.2683 (Rfree = 0.000) for 1500 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 38: After refmac, R = 0.2876 (Rfree = 0.000) for 1495 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 39: After refmac, R = 0.2529 (Rfree = 0.000) for 1487 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 40: After refmac, R = 0.2803 (Rfree = 0.000) for 1483 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.55 3.37 Search for helices and strands: 0 residues in 0 chains, 1499 seeds are put forward NCS extension: 0 residues added, 1499 seeds are put forward Round 1: 64 peptides, 14 chains. Longest chain 7 peptides. Score 0.229 Round 2: 75 peptides, 15 chains. Longest chain 8 peptides. Score 0.277 Round 3: 76 peptides, 13 chains. Longest chain 10 peptides. Score 0.342 Round 4: 82 peptides, 13 chains. Longest chain 10 peptides. Score 0.380 Round 5: 88 peptides, 13 chains. Longest chain 13 peptides. Score 0.416 Taking the results from Round 5 Chains 13, Residues 75, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2851 reflections ( 97.87 % complete ) and 3323 restraints for refining 1519 atoms. 3036 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3014 (Rfree = 0.000) for 1519 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 42: After refmac, R = 0.2952 (Rfree = 0.000) for 1500 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 43: After refmac, R = 0.2921 (Rfree = 0.000) for 1490 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Cycle 44: After refmac, R = 0.2795 (Rfree = 0.000) for 1481 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. Cycle 45: After refmac, R = 0.2538 (Rfree = 0.000) for 1475 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.48 3.30 Search for helices and strands: 0 residues in 0 chains, 1490 seeds are put forward NCS extension: 0 residues added, 1490 seeds are put forward Round 1: 78 peptides, 16 chains. Longest chain 9 peptides. Score 0.269 Round 2: 71 peptides, 16 chains. Longest chain 7 peptides. Score 0.219 Round 3: 81 peptides, 16 chains. Longest chain 9 peptides. Score 0.289 Round 4: 74 peptides, 15 chains. Longest chain 10 peptides. Score 0.270 Round 5: 78 peptides, 15 chains. Longest chain 9 peptides. Score 0.298 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 15, Residues 63, 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. 2851 reflections ( 97.87 % complete ) and 3326 restraints for refining 1511 atoms. 3089 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3094 (Rfree = 0.000) for 1511 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.2750 (Rfree = 0.000) for 1491 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.2825 (Rfree = 0.000) for 1472 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.3182 (Rfree = 0.000) for 1457 atoms. TimeTaking 29.59