Mon 24 Dec 00:42:20 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2nyh-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2nyh-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2nyh-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2nyh-4.0-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2nyh-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2nyh-4.0-parrot-mrncs ############### 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 00:42:25 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/mrncs/ArpWArp/wArpResults/WorkingDir/2nyh-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2nyh-4.0-parrot-mrncs/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 178 and 0 Target number of residues in the AU: 178 Target solvent content: 0.6532 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-4.0-parrot-mrncs.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-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 1872 target number of atoms Had to go as low as 0.85 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 4.000 Wilson plot Bfac: 79.66 2464 reflections ( 97.66 % complete ) and 0 restraints for refining 2062 atoms. Observations/parameters ratio is 0.30 ------------------------------------------------------ Starting model: R = 0.3586 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3551 (Rfree = 0.000) for 2062 atoms. Found 9 (9 requested) and removed 20 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.82 3.62 Search for helices and strands: 0 residues in 0 chains, 2071 seeds are put forward NCS extension: 0 residues added, 2071 seeds are put forward Round 1: 56 peptides, 13 chains. Longest chain 7 peptides. Score 0.199 Round 2: 89 peptides, 18 chains. Longest chain 8 peptides. Score 0.286 Round 3: 103 peptides, 19 chains. Longest chain 10 peptides. Score 0.348 Round 4: 113 peptides, 19 chains. Longest chain 12 peptides. Score 0.407 Round 5: 115 peptides, 19 chains. Longest chain 20 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 ------------------------------------------------------ 2464 reflections ( 97.66 % complete ) and 3802 restraints for refining 1641 atoms. 3437 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3382 (Rfree = 0.000) for 1641 atoms. Found 7 (7 requested) and removed 30 (3 requested) atoms. Cycle 2: After refmac, R = 0.3110 (Rfree = 0.000) for 1596 atoms. Found 7 (7 requested) and removed 14 (3 requested) atoms. Cycle 3: After refmac, R = 0.3318 (Rfree = 0.000) for 1571 atoms. Found 7 (7 requested) and removed 15 (3 requested) atoms. Cycle 4: After refmac, R = 0.3219 (Rfree = 0.000) for 1549 atoms. Found 7 (7 requested) and removed 16 (3 requested) atoms. Cycle 5: After refmac, R = 0.3089 (Rfree = 0.000) for 1518 atoms. Found 7 (7 requested) and removed 13 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.79 3.59 Search for helices and strands: 0 residues in 0 chains, 1554 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 1578 seeds are put forward Round 1: 92 peptides, 18 chains. Longest chain 8 peptides. Score 0.305 Round 2: 112 peptides, 17 chains. Longest chain 12 peptides. Score 0.451 Round 3: 109 peptides, 16 chains. Longest chain 12 peptides. Score 0.459 Round 4: 104 peptides, 16 chains. Longest chain 13 peptides. Score 0.431 Round 5: 97 peptides, 15 chains. Longest chain 13 peptides. Score 0.416 Taking the results from Round 3 Chains 16, Residues 93, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 2464 reflections ( 97.66 % complete ) and 3407 restraints for refining 1593 atoms. 2995 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3097 (Rfree = 0.000) for 1593 atoms. Found 7 (7 requested) and removed 12 (3 requested) atoms. Cycle 7: After refmac, R = 0.2971 (Rfree = 0.000) for 1566 atoms. Found 7 (7 requested) and removed 11 (3 requested) atoms. Cycle 8: After refmac, R = 0.2963 (Rfree = 0.000) for 1538 atoms. Found 7 (7 requested) and removed 10 (3 requested) atoms. Cycle 9: After refmac, R = 0.3001 (Rfree = 0.000) for 1522 atoms. Found 7 (7 requested) and removed 13 (3 requested) atoms. Cycle 10: After refmac, R = 0.2828 (Rfree = 0.000) for 1498 atoms. Found 5 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.77 3.57 Search for helices and strands: 0 residues in 0 chains, 1529 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 1544 seeds are put forward Round 1: 94 peptides, 17 chains. Longest chain 11 peptides. Score 0.345 Round 2: 109 peptides, 19 chains. Longest chain 11 peptides. Score 0.384 Round 3: 117 peptides, 17 chains. Longest chain 12 peptides. Score 0.478 Round 4: 103 peptides, 15 chains. Longest chain 10 peptides. Score 0.451 Round 5: 104 peptides, 15 chains. Longest chain 12 peptides. Score 0.456 Taking the results from Round 3 Chains 17, Residues 100, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 2464 reflections ( 97.66 % complete ) and 3424 restraints for refining 1566 atoms. 3014 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2843 (Rfree = 0.000) for 1566 atoms. Found 7 (7 requested) and removed 11 (3 requested) atoms. Cycle 12: After refmac, R = 0.3059 (Rfree = 0.000) for 1537 atoms. Found 7 (7 requested) and removed 16 (3 requested) atoms. Cycle 13: After refmac, R = 0.2842 (Rfree = 0.000) for 1502 atoms. Found 6 (7 requested) and removed 9 (3 requested) atoms. Cycle 14: After refmac, R = 0.3178 (Rfree = 0.000) for 1479 atoms. Found 7 (7 requested) and removed 18 (3 requested) atoms. Cycle 15: After refmac, R = 0.2866 (Rfree = 0.000) for 1449 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.84 3.64 Search for helices and strands: 0 residues in 0 chains, 1500 seeds are put forward NCS extension: 0 residues added, 1500 seeds are put forward Round 1: 95 peptides, 18 chains. Longest chain 9 peptides. Score 0.325 Round 2: 97 peptides, 15 chains. Longest chain 11 peptides. Score 0.416 Round 3: 92 peptides, 16 chains. Longest chain 11 peptides. Score 0.360 Round 4: 92 peptides, 15 chains. Longest chain 9 peptides. Score 0.387 Round 5: 95 peptides, 15 chains. Longest chain 15 peptides. Score 0.405 Taking the results from Round 2 Chains 15, Residues 82, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2464 reflections ( 97.66 % complete ) and 3344 restraints for refining 1489 atoms. 3031 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3395 (Rfree = 0.000) for 1489 atoms. Found 7 (7 requested) and removed 17 (3 requested) atoms. Cycle 17: After refmac, R = 0.3045 (Rfree = 0.000) for 1460 atoms. Found 7 (7 requested) and removed 12 (3 requested) atoms. Cycle 18: After refmac, R = 0.2948 (Rfree = 0.000) for 1443 atoms. Found 6 (6 requested) and removed 9 (3 requested) atoms. Cycle 19: After refmac, R = 0.3046 (Rfree = 0.000) for 1426 atoms. Found 6 (6 requested) and removed 16 (3 requested) atoms. Cycle 20: After refmac, R = 0.2837 (Rfree = 0.000) for 1403 atoms. Found 5 (6 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.73 3.54 Search for helices and strands: 0 residues in 0 chains, 1431 seeds are put forward NCS extension: 0 residues added, 1431 seeds are put forward Round 1: 73 peptides, 15 chains. Longest chain 7 peptides. Score 0.263 Round 2: 99 peptides, 18 chains. Longest chain 8 peptides. Score 0.350 Round 3: 103 peptides, 16 chains. Longest chain 15 peptides. Score 0.425 Round 4: 108 peptides, 16 chains. Longest chain 11 peptides. Score 0.454 Round 5: 108 peptides, 16 chains. Longest chain 15 peptides. Score 0.454 Taking the results from Round 5 Chains 16, Residues 92, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2464 reflections ( 97.66 % complete ) and 3365 restraints for refining 1536 atoms. 3013 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2882 (Rfree = 0.000) for 1536 atoms. Found 7 (7 requested) and removed 9 (3 requested) atoms. Cycle 22: After refmac, R = 0.2861 (Rfree = 0.000) for 1520 atoms. Found 7 (7 requested) and removed 14 (3 requested) atoms. Cycle 23: After refmac, R = 0.2724 (Rfree = 0.000) for 1499 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 24: After refmac, R = 0.2742 (Rfree = 0.000) for 1491 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 25: After refmac, R = 0.3113 (Rfree = 0.000) for 1482 atoms. Found 7 (7 requested) and removed 12 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.79 3.59 Search for helices and strands: 0 residues in 0 chains, 1501 seeds are put forward NCS extension: 0 residues added, 1501 seeds are put forward Round 1: 89 peptides, 17 chains. Longest chain 8 peptides. Score 0.314 Round 2: 92 peptides, 14 chains. Longest chain 9 peptides. Score 0.413 Round 3: 87 peptides, 13 chains. Longest chain 16 peptides. Score 0.410 Round 4: 98 peptides, 14 chains. Longest chain 17 peptides. Score 0.448 Round 5: 91 peptides, 14 chains. Longest chain 14 peptides. Score 0.407 Taking the results from Round 4 Chains 14, Residues 84, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2464 reflections ( 97.66 % complete ) and 3479 restraints for refining 1560 atoms. 3157 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3018 (Rfree = 0.000) for 1560 atoms. Found 7 (7 requested) and removed 19 (3 requested) atoms. Cycle 27: After refmac, R = 0.2872 (Rfree = 0.000) for 1528 atoms. Found 7 (7 requested) and removed 13 (3 requested) atoms. Cycle 28: After refmac, R = 0.3080 (Rfree = 0.000) for 1508 atoms. Found 7 (7 requested) and removed 10 (3 requested) atoms. Cycle 29: After refmac, R = 0.2774 (Rfree = 0.000) for 1491 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. Cycle 30: After refmac, R = 0.2985 (Rfree = 0.000) for 1478 atoms. Found 7 (7 requested) and removed 10 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.72 3.53 Search for helices and strands: 0 residues in 0 chains, 1503 seeds are put forward NCS extension: 0 residues added, 1503 seeds are put forward Round 1: 78 peptides, 18 chains. Longest chain 7 peptides. Score 0.210 Round 2: 92 peptides, 18 chains. Longest chain 9 peptides. Score 0.305 Round 3: 98 peptides, 15 chains. Longest chain 12 peptides. Score 0.422 Round 4: 93 peptides, 16 chains. Longest chain 14 peptides. Score 0.366 Round 5: 80 peptides, 14 chains. Longest chain 12 peptides. Score 0.339 Taking the results from Round 3 Chains 15, Residues 83, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2464 reflections ( 97.66 % complete ) and 3230 restraints for refining 1505 atoms. 2913 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3167 (Rfree = 0.000) for 1505 atoms. Found 7 (7 requested) and removed 15 (3 requested) atoms. Cycle 32: After refmac, R = 0.3187 (Rfree = 0.000) for 1488 atoms. Found 7 (7 requested) and removed 16 (3 requested) atoms. Cycle 33: After refmac, R = 0.2811 (Rfree = 0.000) for 1469 atoms. Found 7 (7 requested) and removed 13 (3 requested) atoms. Cycle 34: After refmac, R = 0.2784 (Rfree = 0.000) for 1454 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. Cycle 35: After refmac, R = 0.3209 (Rfree = 0.000) for 1446 atoms. Found 6 (6 requested) and removed 16 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.80 3.60 Search for helices and strands: 0 residues in 0 chains, 1477 seeds are put forward NCS extension: 0 residues added, 1477 seeds are put forward Round 1: 65 peptides, 14 chains. Longest chain 6 peptides. Score 0.236 Round 2: 70 peptides, 14 chains. Longest chain 7 peptides. Score 0.272 Round 3: 74 peptides, 13 chains. Longest chain 11 peptides. Score 0.329 Round 4: 73 peptides, 14 chains. Longest chain 7 peptides. Score 0.293 Round 5: 76 peptides, 14 chains. Longest chain 8 peptides. Score 0.313 Taking the results from Round 3 Chains 13, Residues 61, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2464 reflections ( 97.66 % complete ) and 3066 restraints for refining 1401 atoms. 2835 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3166 (Rfree = 0.000) for 1401 atoms. Found 6 (6 requested) and removed 9 (3 requested) atoms. Cycle 37: After refmac, R = 0.3241 (Rfree = 0.000) for 1386 atoms. Found 6 (6 requested) and removed 16 (3 requested) atoms. Cycle 38: After refmac, R = 0.3248 (Rfree = 0.000) for 1361 atoms. Found 6 (6 requested) and removed 11 (3 requested) atoms. Cycle 39: After refmac, R = 0.2813 (Rfree = 0.000) for 1346 atoms. Found 6 (6 requested) and removed 12 (3 requested) atoms. Cycle 40: After refmac, R = 0.2800 (Rfree = 0.000) for 1339 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.78 3.58 Search for helices and strands: 0 residues in 0 chains, 1368 seeds are put forward NCS extension: 0 residues added, 1368 seeds are put forward Round 1: 63 peptides, 14 chains. Longest chain 7 peptides. Score 0.221 Round 2: 71 peptides, 14 chains. Longest chain 8 peptides. Score 0.279 Round 3: 76 peptides, 13 chains. Longest chain 10 peptides. Score 0.342 Round 4: 76 peptides, 14 chains. Longest chain 7 peptides. Score 0.313 Round 5: 83 peptides, 12 chains. Longest chain 18 peptides. Score 0.414 Taking the results from Round 5 Chains 12, Residues 71, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2464 reflections ( 97.66 % complete ) and 3073 restraints for refining 1408 atoms. 2801 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2999 (Rfree = 0.000) for 1408 atoms. Found 6 (6 requested) and removed 18 (3 requested) atoms. Cycle 42: After refmac, R = 0.2904 (Rfree = 0.000) for 1385 atoms. Found 6 (6 requested) and removed 9 (3 requested) atoms. Cycle 43: After refmac, R = 0.2803 (Rfree = 0.000) for 1371 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. Cycle 44: After refmac, R = 0.2786 (Rfree = 0.000) for 1355 atoms. Found 6 (6 requested) and removed 3 (3 requested) atoms. Cycle 45: After refmac, R = 0.2678 (Rfree = 0.000) for 1351 atoms. Found 6 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.73 3.54 Search for helices and strands: 0 residues in 0 chains, 1384 seeds are put forward NCS extension: 32 residues added (1 deleted due to clashes), 1416 seeds are put forward Round 1: 63 peptides, 13 chains. Longest chain 7 peptides. Score 0.253 Round 2: 85 peptides, 15 chains. Longest chain 14 peptides. Score 0.343 Round 3: 86 peptides, 16 chains. Longest chain 13 peptides. Score 0.322 Round 4: 78 peptides, 11 chains. Longest chain 13 peptides. Score 0.411 Round 5: 73 peptides, 12 chains. Longest chain 13 peptides. Score 0.351 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 11, Residues 67, 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-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2464 reflections ( 97.66 % complete ) and 3000 restraints for refining 1403 atoms. 2743 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3157 (Rfree = 0.000) for 1403 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.2865 (Rfree = 0.000) for 1380 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.3259 (Rfree = 0.000) for 1367 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.3080 (Rfree = 0.000) for 1354 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Writing output files ... TimeTaking 21.93