null 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 1vpz-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vpz-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vpz-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vpz-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/1vpz-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vpz-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 22:22:59 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/1vpz-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vpz-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 91 and 0 Target number of residues in the AU: 91 Target solvent content: 0.6402 Checking the provided sequence file Detected sequence length: 73 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 146 Adjusted target solvent content: 0.42 Input MTZ file: 1vpz-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: 49.075 56.647 98.468 90.000 90.000 90.000 Input sequence file: 1vpz-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 1168 target number of atoms Had to go as low as 0.50 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: 24.580 3.200 Wilson plot Bfac: 71.57 2402 reflections ( 98.40 % complete ) and 0 restraints for refining 1289 atoms. Observations/parameters ratio is 0.47 ------------------------------------------------------ Starting model: R = 0.3618 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3633 (Rfree = 0.000) for 1289 atoms. Found 11 (11 requested) and removed 41 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.29 3.66 Search for helices and strands: 0 residues in 0 chains, 1263 seeds are put forward NCS extension: 0 residues added, 1263 seeds are put forward Round 1: 30 peptides, 7 chains. Longest chain 5 peptides. Score 0.199 Round 2: 38 peptides, 7 chains. Longest chain 11 peptides. Score 0.315 Round 3: 54 peptides, 9 chains. Longest chain 12 peptides. Score 0.406 Round 4: 48 peptides, 9 chains. Longest chain 11 peptides. Score 0.333 Round 5: 53 peptides, 10 chains. Longest chain 11 peptides. Score 0.342 Taking the results from Round 3 Chains 9, Residues 45, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2402 reflections ( 98.40 % complete ) and 2445 restraints for refining 1004 atoms. 2274 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3783 (Rfree = 0.000) for 1004 atoms. Found 9 (9 requested) and removed 36 (4 requested) atoms. Cycle 2: After refmac, R = 0.3745 (Rfree = 0.000) for 964 atoms. Found 8 (8 requested) and removed 18 (4 requested) atoms. Cycle 3: After refmac, R = 0.3856 (Rfree = 0.000) for 943 atoms. Found 8 (8 requested) and removed 15 (4 requested) atoms. Cycle 4: After refmac, R = 0.3834 (Rfree = 0.000) for 931 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Cycle 5: After refmac, R = 0.3824 (Rfree = 0.000) for 927 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.18 3.54 Search for helices and strands: 0 residues in 0 chains, 935 seeds are put forward NCS extension: 0 residues added, 935 seeds are put forward Round 1: 29 peptides, 7 chains. Longest chain 5 peptides. Score 0.183 Round 2: 43 peptides, 9 chains. Longest chain 8 peptides. Score 0.267 Round 3: 41 peptides, 7 chains. Longest chain 10 peptides. Score 0.354 Round 4: 29 peptides, 5 chains. Longest chain 8 peptides. Score 0.312 Round 5: 31 peptides, 5 chains. Longest chain 9 peptides. Score 0.340 Taking the results from Round 3 Chains 7, Residues 34, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2402 reflections ( 98.40 % complete ) and 1891 restraints for refining 811 atoms. 1762 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3760 (Rfree = 0.000) for 811 atoms. Found 7 (7 requested) and removed 16 (3 requested) atoms. Cycle 7: After refmac, R = 0.4075 (Rfree = 0.000) for 800 atoms. Found 7 (7 requested) and removed 17 (3 requested) atoms. Cycle 8: After refmac, R = 0.3846 (Rfree = 0.000) for 786 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 9: After refmac, R = 0.3730 (Rfree = 0.000) for 784 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 10: After refmac, R = 0.3733 (Rfree = 0.000) for 784 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 4.39 4.89 Search for helices and strands: 0 residues in 0 chains, 820 seeds are put forward NCS extension: 0 residues added, 820 seeds are put forward Round 1: 35 peptides, 6 chains. Longest chain 9 peptides. Score 0.333 Round 2: 39 peptides, 8 chains. Longest chain 6 peptides. Score 0.270 Round 3: 46 peptides, 9 chains. Longest chain 8 peptides. Score 0.307 Round 4: 49 peptides, 7 chains. Longest chain 12 peptides. Score 0.451 Round 5: 59 peptides, 9 chains. Longest chain 12 peptides. Score 0.463 Taking the results from Round 5 Chains 9, Residues 50, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2402 reflections ( 98.40 % complete ) and 1466 restraints for refining 735 atoms. 1275 conditional restraints added. Observations/parameters ratio is 0.82 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3385 (Rfree = 0.000) for 735 atoms. Found 6 (6 requested) and removed 10 (3 requested) atoms. Cycle 12: After refmac, R = 0.3322 (Rfree = 0.000) for 725 atoms. Found 6 (6 requested) and removed 10 (3 requested) atoms. Cycle 13: After refmac, R = 0.3438 (Rfree = 0.000) for 717 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 14: After refmac, R = 0.3433 (Rfree = 0.000) for 716 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 15: After refmac, R = 0.3255 (Rfree = 0.000) for 716 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.63 2.93 Search for helices and strands: 0 residues in 0 chains, 732 seeds are put forward NCS extension: 0 residues added, 732 seeds are put forward Round 1: 61 peptides, 13 chains. Longest chain 7 peptides. Score 0.285 Round 2: 74 peptides, 13 chains. Longest chain 11 peptides. Score 0.438 Round 3: 68 peptides, 12 chains. Longest chain 10 peptides. Score 0.419 Round 4: 70 peptides, 11 chains. Longest chain 12 peptides. Score 0.487 Round 5: 66 peptides, 12 chains. Longest chain 10 peptides. Score 0.396 Taking the results from Round 4 Chains 11, Residues 59, Estimated correctness of the model 7.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2402 reflections ( 98.40 % complete ) and 1698 restraints for refining 792 atoms. 1473 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3654 (Rfree = 0.000) for 792 atoms. Found 7 (7 requested) and removed 13 (3 requested) atoms. Cycle 17: After refmac, R = 0.3874 (Rfree = 0.000) for 782 atoms. Found 7 (7 requested) and removed 14 (3 requested) atoms. Cycle 18: After refmac, R = 0.3647 (Rfree = 0.000) for 772 atoms. Found 6 (6 requested) and removed 9 (3 requested) atoms. Cycle 19: After refmac, R = 0.3277 (Rfree = 0.000) for 768 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. Cycle 20: After refmac, R = 0.3506 (Rfree = 0.000) for 770 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 4.47 4.98 Search for helices and strands: 0 residues in 0 chains, 797 seeds are put forward NCS extension: 7 residues added (2 deleted due to clashes), 804 seeds are put forward Round 1: 47 peptides, 10 chains. Longest chain 7 peptides. Score 0.265 Round 2: 52 peptides, 10 chains. Longest chain 11 peptides. Score 0.330 Round 3: 54 peptides, 9 chains. Longest chain 10 peptides. Score 0.406 Round 4: 54 peptides, 9 chains. Longest chain 11 peptides. Score 0.406 Round 5: 57 peptides, 9 chains. Longest chain 10 peptides. Score 0.441 Taking the results from Round 5 Chains 9, Residues 48, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2402 reflections ( 98.40 % complete ) and 1789 restraints for refining 807 atoms. 1606 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3414 (Rfree = 0.000) for 807 atoms. Found 7 (7 requested) and removed 14 (3 requested) atoms. Cycle 22: After refmac, R = 0.3282 (Rfree = 0.000) for 793 atoms. Found 7 (7 requested) and removed 13 (3 requested) atoms. Cycle 23: After refmac, R = 0.3145 (Rfree = 0.000) for 782 atoms. Found 5 (7 requested) and removed 3 (3 requested) atoms. Cycle 24: After refmac, R = 0.3026 (Rfree = 0.000) for 784 atoms. Found 2 (7 requested) and removed 4 (3 requested) atoms. Cycle 25: After refmac, R = 0.3000 (Rfree = 0.000) for 781 atoms. Found 2 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.33 3.71 Search for helices and strands: 0 residues in 0 chains, 789 seeds are put forward NCS extension: 0 residues added, 789 seeds are put forward Round 1: 49 peptides, 10 chains. Longest chain 9 peptides. Score 0.291 Round 2: 56 peptides, 10 chains. Longest chain 10 peptides. Score 0.379 Round 3: 58 peptides, 11 chains. Longest chain 7 peptides. Score 0.352 Round 4: 59 peptides, 9 chains. Longest chain 11 peptides. Score 0.463 Round 5: 68 peptides, 12 chains. Longest chain 9 peptides. Score 0.419 Taking the results from Round 4 Chains 9, Residues 50, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2402 reflections ( 98.40 % complete ) and 1797 restraints for refining 822 atoms. 1606 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3473 (Rfree = 0.000) for 822 atoms. Found 5 (7 requested) and removed 10 (3 requested) atoms. Cycle 27: After refmac, R = 0.3277 (Rfree = 0.000) for 811 atoms. Found 7 (7 requested) and removed 3 (3 requested) atoms. Cycle 28: After refmac, R = 0.3051 (Rfree = 0.000) for 811 atoms. Found 6 (7 requested) and removed 7 (3 requested) atoms. Cycle 29: After refmac, R = 0.2981 (Rfree = 0.000) for 809 atoms. Found 2 (7 requested) and removed 4 (3 requested) atoms. Cycle 30: After refmac, R = 0.2926 (Rfree = 0.000) for 806 atoms. Found 2 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.37 3.75 Search for helices and strands: 0 residues in 0 chains, 826 seeds are put forward NCS extension: 0 residues added, 826 seeds are put forward Round 1: 35 peptides, 6 chains. Longest chain 10 peptides. Score 0.333 Round 2: 57 peptides, 11 chains. Longest chain 8 peptides. Score 0.339 Round 3: 51 peptides, 8 chains. Longest chain 14 peptides. Score 0.423 Round 4: 52 peptides, 9 chains. Longest chain 15 peptides. Score 0.382 Round 5: 59 peptides, 10 chains. Longest chain 12 peptides. Score 0.414 Taking the results from Round 3 Chains 8, Residues 43, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2402 reflections ( 98.40 % complete ) and 1636 restraints for refining 773 atoms. 1472 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3343 (Rfree = 0.000) for 773 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Cycle 32: After refmac, R = 0.3204 (Rfree = 0.000) for 768 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 33: After refmac, R = 0.3001 (Rfree = 0.000) for 768 atoms. Found 2 (6 requested) and removed 3 (3 requested) atoms. Cycle 34: After refmac, R = 0.3119 (Rfree = 0.000) for 759 atoms. Found 6 (6 requested) and removed 3 (3 requested) atoms. Cycle 35: After refmac, R = 0.3010 (Rfree = 0.000) for 761 atoms. Found 3 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.57 3.98 Search for helices and strands: 0 residues in 0 chains, 787 seeds are put forward NCS extension: 0 residues added, 787 seeds are put forward Round 1: 52 peptides, 11 chains. Longest chain 7 peptides. Score 0.276 Round 2: 59 peptides, 13 chains. Longest chain 8 peptides. Score 0.260 Round 3: 63 peptides, 11 chains. Longest chain 14 peptides. Score 0.411 Round 4: 65 peptides, 12 chains. Longest chain 9 peptides. Score 0.385 Round 5: 68 peptides, 12 chains. Longest chain 14 peptides. Score 0.419 Taking the results from Round 5 Chains 12, Residues 56, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2402 reflections ( 98.40 % complete ) and 1433 restraints for refining 754 atoms. 1221 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 36: After refmac, R = 0.4373 (Rfree = 0.000) for 754 atoms. Found 6 (6 requested) and removed 29 (3 requested) atoms. Cycle 37: After refmac, R = 0.3642 (Rfree = 0.000) for 725 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 38: After refmac, R = 0.3382 (Rfree = 0.000) for 719 atoms. Found 1 (6 requested) and removed 7 (3 requested) atoms. Cycle 39: After refmac, R = 0.3200 (Rfree = 0.000) for 707 atoms. Found 1 (6 requested) and removed 3 (3 requested) atoms. Cycle 40: After refmac, R = 0.3349 (Rfree = 0.000) for 705 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.51 3.91 Search for helices and strands: 0 residues in 0 chains, 731 seeds are put forward NCS extension: 0 residues added, 731 seeds are put forward Round 1: 39 peptides, 7 chains. Longest chain 11 peptides. Score 0.328 Round 2: 60 peptides, 12 chains. Longest chain 9 peptides. Score 0.325 Round 3: 61 peptides, 13 chains. Longest chain 7 peptides. Score 0.285 Round 4: 62 peptides, 12 chains. Longest chain 8 peptides. Score 0.349 Round 5: 67 peptides, 13 chains. Longest chain 7 peptides. Score 0.359 Taking the results from Round 5 Chains 13, Residues 54, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2402 reflections ( 98.40 % complete ) and 1500 restraints for refining 740 atoms. 1297 conditional restraints added. Observations/parameters ratio is 0.81 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3490 (Rfree = 0.000) for 740 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. Cycle 42: After refmac, R = 0.3390 (Rfree = 0.000) for 736 atoms. Found 1 (6 requested) and removed 6 (3 requested) atoms. Cycle 43: After refmac, R = 0.3446 (Rfree = 0.000) for 726 atoms. Found 6 (6 requested) and removed 3 (3 requested) atoms. Cycle 44: After refmac, R = 0.3265 (Rfree = 0.000) for 727 atoms. Found 5 (6 requested) and removed 4 (3 requested) atoms. Cycle 45: After refmac, R = 0.3159 (Rfree = 0.000) for 727 atoms. Found 2 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.65 4.06 Search for helices and strands: 0 residues in 0 chains, 739 seeds are put forward NCS extension: 0 residues added, 739 seeds are put forward Round 1: 48 peptides, 10 chains. Longest chain 7 peptides. Score 0.278 Round 2: 55 peptides, 11 chains. Longest chain 8 peptides. Score 0.314 Round 3: 59 peptides, 11 chains. Longest chain 8 peptides. Score 0.364 Round 4: 54 peptides, 11 chains. Longest chain 8 peptides. Score 0.302 Round 5: 60 peptides, 12 chains. Longest chain 8 peptides. Score 0.325 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 11, Residues 48, 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 1vpz-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2402 reflections ( 98.40 % complete ) and 1478 restraints for refining 750 atoms. 1297 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3502 (Rfree = 0.000) for 750 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.3192 (Rfree = 0.000) for 745 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.3357 (Rfree = 0.000) for 741 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.3127 (Rfree = 0.000) for 737 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:45:13 GMT 2018 Job finished. TimeTaking 22.4 Used memory is bytes: 14201600